DC-Build-Header: trinityrnaseq 2.2.0+dfsg-2 / 2016-08-29 15:50:29 +0000 DC-Task: type:rebuild-binarch-only source:trinityrnaseq version:2.2.0+dfsg-2 chroot:unstable esttime:986 logfile:/tmp/trinityrnaseq_2.2.0+dfsg-2_unstable_clang3.8.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang trinityrnaseq_2.2.0+dfsg-2' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-15-93.eu-central-1.compute.internal +==============================================================================+ | trinityrnaseq 2.2.0+dfsg-2 (amd64) Mon, 29 Aug 2016 15:50:29 +0000 | +==============================================================================+ Package: trinityrnaseq Version: 2.2.0+dfsg-2 Source Version: 2.2.0+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-34ed862d-57f4-4735-a6c4-f5f75011e659' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.8 + echo 'Install of clang-3.8' Install of clang-3.8 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [209 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en [5451 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0319.00.pdiff [16.7 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0319.00.pdiff [13.2 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Fetched 5755 kB in 2s (1981 kB/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges + apt-get install --yes --no-install-recommends --force-yes clang-3.8 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.8-doc Recommended packages: llvm-3.8-dev python The following NEW packages will be installed: clang-3.8 libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. Need to get 38.3 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20150325-1+b1 [85.2 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.8 amd64 1:3.8.1-9 [10.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 6.2.0-1 [110 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.2.0-1 [394 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.8 amd64 1:3.8.1-9 [4188 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.8-dev amd64 1:3.8.1-9 [1477 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.8 amd64 1:3.8.1-9 [21.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.3 MB in 0s (97.5 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9446 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../1-libedit2_3.1-20150325-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20150325-1+b1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../2-libffi6_3.2.1-4_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-4) ... Selecting previously unselected package libllvm3.8:amd64. Preparing to unpack .../3-libllvm3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libllvm3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../4-libobjc4_6.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (6.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../5-libobjc-6-dev_6.2.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.2.0-1) ... Selecting previously unselected package libclang1-3.8:amd64. Preparing to unpack .../6-libclang1-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libclang1-3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libclang-common-3.8-dev. Preparing to unpack .../7-libclang-common-3.8-dev_1%3a3.8.1-9_amd64.deb ... Unpacking libclang-common-3.8-dev (1:3.8.1-9) ... Selecting previously unselected package clang-3.8. Preparing to unpack .../8-clang-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking clang-3.8 (1:3.8.1-9) ... Setting up libobjc4:amd64 (6.2.0-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up libobjc-6-dev:amd64 (6.2.0-1) ... Setting up libffi6:amd64 (3.2.1-4) ... Setting up libedit2:amd64 (3.1-20150325-1+b1) ... Setting up libllvm3.8:amd64 (1:3.8.1-9) ... Setting up libclang-common-3.8-dev (1:3.8.1-9) ... Setting up libclang1-3.8:amd64 (1:3.8.1-9) ... Setting up clang-3.8 (1:3.8.1-9) ... Processing triggers for libc-bin (2.23-5) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. W: No sandbox user '_apt' on the system, can not drop privileges + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.8 g++-4.6 + ln -s clang-3.8 gcc-4.6 + ln -s clang-3.8 cpp-4.6 + ln -s clang-3.8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.8 g++-4.7 + ln -s clang-3.8 gcc-4.7 + ln -s clang-3.8 cpp-4.7 + ln -s clang-3.8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.8 g++-4.8 + ln -s clang-3.8 gcc-4.8 + ln -s clang-3.8 cpp-4.8 + ln -s clang-3.8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.8 g++-4.9 + ln -s clang-3.8 gcc-4.9 + ln -s clang-3.8 cpp-4.9 + ln -s clang-3.8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.8 g++-5 + ln -s clang-3.8 gcc-5 + ln -s clang-3.8 cpp-5 + ln -s clang-3.8 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.8 g++-6 + ln -s clang-3.8 gcc-6 + ln -s clang-3.8 cpp-6 + ln -s clang-3.8 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + cd - /build/trinityrnaseq-bErWHV + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: linux-libc-dev 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1158 kB of archives. After this operation, 60.4 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 linux-libc-dev amd64 4.7.2-1 [1158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1158 kB in 0s (70.4 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9769 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_4.7.2-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.7.2-1) over (4.6.4-1) ... Setting up linux-libc-dev:amd64 (4.7.2-1) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'trinityrnaseq' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/trinityrnaseq.git Please use: git clone https://anonscm.debian.org/git/debian-med/trinityrnaseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 MB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main trinityrnaseq 2.2.0+dfsg-2 (dsc) [2274 B] Get:2 http://127.0.0.1:9999/debian unstable/main trinityrnaseq 2.2.0+dfsg-2 (tar) [155 MB] Get:3 http://127.0.0.1:9999/debian unstable/main trinityrnaseq 2.2.0+dfsg-2 (diff) [17.1 kB] Fetched 155 MB in 3s (42.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/trinityrnaseq-bErWHV/trinityrnaseq-2.2.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/trinityrnaseq-bErWHV' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-hII6BF/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-hII6BF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-hII6BF/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-hII6BF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-hII6BF/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-hII6BF/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 774 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-hII6BF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 774 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 9775 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf, automake1.11, jellyfish (>= 2.1.4), libjung-free-java, javahelper, libgetopt-java, default-jdk, parafly, libjs-jquery, jaligner, libhts-dev Filtered Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf, automake1.11, jellyfish (>= 2.1.4), libjung-free-java, javahelper, libgetopt-java, default-jdk, parafly, libjs-jquery, jaligner, libhts-dev dpkg-deb: building package 'sbuild-build-depends-trinityrnaseq-dummy' in '/<>/resolver-W8x41w/apt_archive/sbuild-build-depends-trinityrnaseq-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-trinityrnaseq-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-W8x41w/apt_archive ./ InRelease Get:2 copy:/<>/resolver-W8x41w/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-W8x41w/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-W8x41w/apt_archive ./ Sources [442 B] Get:5 copy:/<>/resolver-W8x41w/apt_archive ./ Packages [530 B] Fetched 1929 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Install trinityrnaseq build dependencies (apt-based resolver) ------------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adwaita-icon-theme autoconf automake automake1.11 autopoint autotools-dev bsdmainutils ca-certificates ca-certificates-java dconf-gsettings-backend dconf-service dctrl-tools debhelper default-jdk default-jdk-headless default-jre default-jre-headless devscripts dh-autoreconf dh-python dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base glib-networking glib-networking-common glib-networking-services gnome-icon-theme groff-base gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme intltool-debian jaligner java-common javahelper jellyfish libarchive-zip-perl libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libcairo-gobject2 libcairo2 libcap2 libcolord2 libcolt-free-java libcommons-collections4-java libconcurrent-java libcroco3 libcups2 libcurl3-gnutls libdatrie1 libdbus-1-3 libdconf1 libdrm2 libegl1-mesa libepoxy0 libexpat1 libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfontenc1 libfreetype6 libgbm1 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgif7 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhts-dev libhts1 libice6 libicu57 libidn11 libjbig0 libjellyfish-2.0-2 libjpeg62-turbo libjs-jquery libjson-c3 libjson-glib-1.0-0 libjson-glib-1.0-common libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14 libnspr4 libnss3 libogg0 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpipeline1 libpixman-1-0 libpng16-16 libproxy1v5 libpulse0 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libreadline6 librest-0.7-0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsndfile1 libsoup-gnome2.4-1 libsoup2.4-1 libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libthai-data libthai0 libtiff5 libtimedate-perl libtool libunistring0 libvecmath-java libvorbis0a libvorbisenc2 libwayland-client0 libwayland-cursor0 libwayland-egl1-mesa libwayland-server0 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 lsb-base m4 man-db mime-support openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless openssl parafly po-debconf python3 python3-minimal python3.5 python3.5-minimal readline-common shared-mime-info ucf x11-common x11-utils xkb-data Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation debtags dh-make bsd-mailx | mailx cvs-buildpackage diffoscope devscripts-el dose-extra gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl libterm-size-perl libyaml-syck-perl mozilla-devscripts mutt reprotest ssh-client svn-buildpackage w3m gettext-doc libasprintf-dev libgettextpo-dev groff cvs gawk tofrodos libasound2-plugins alsa-utils colord libcommons-collections4-java-doc cups-common libgetopt-java-doc gnutls-bin krb5-doc krb5-user gvfs liblcms2-utils pcscd pulseaudio librsvg2-bin libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser openjdk-8-demo openjdk-8-source visualvm icedtea-8-plugin openjdk-8-jre-jamvm libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python3.5-venv python3.5-doc binfmt-support readline-doc mesa-utils Recommended packages: default-java-plugin at dput | dupload gnupg | gnupg2 libdistro-info-perl libencode-locale-perl liburi-perl libwww-perl licensecheck lintian patchutils python3-debian python3-magic strace unzip wdiff wget | curl debian-keyring equivs liblwp-protocol-https-perl libsoap-lite-perl curl | wget | lynx-cur at-spi2-core dbus libgl1-mesa-dri libglib2.0-data xdg-user-dirs libgtk-3-bin libgail-common libgtk2.0-bin javascript-common krb5-locales libsasl2-modules libltdl-dev tcpd xml-core libxt-dev libgnome-2-0 libgnomevfs2-0 libgconf-2-4 fonts-dejavu-extra libmail-sendmail-perl The following NEW packages will be installed: adwaita-icon-theme autoconf automake automake1.11 autopoint autotools-dev bsdmainutils ca-certificates ca-certificates-java dconf-gsettings-backend dconf-service dctrl-tools debhelper default-jdk default-jdk-headless default-jre default-jre-headless devscripts dh-autoreconf dh-python dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base glib-networking glib-networking-common glib-networking-services gnome-icon-theme groff-base gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme intltool-debian jaligner java-common javahelper jellyfish libarchive-zip-perl libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libcairo-gobject2 libcairo2 libcap2 libcolord2 libcolt-free-java libcommons-collections4-java libconcurrent-java libcroco3 libcups2 libcurl3-gnutls libdatrie1 libdbus-1-3 libdconf1 libdrm2 libegl1-mesa libepoxy0 libexpat1 libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfontenc1 libfreetype6 libgbm1 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgif7 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhts-dev libhts1 libice6 libicu57 libidn11 libjbig0 libjellyfish-2.0-2 libjpeg62-turbo libjs-jquery libjson-c3 libjson-glib-1.0-0 libjson-glib-1.0-common libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14 libnspr4 libnss3 libogg0 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpipeline1 libpixman-1-0 libpng16-16 libproxy1v5 libpulse0 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libreadline6 librest-0.7-0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsndfile1 libsoup-gnome2.4-1 libsoup2.4-1 libsqlite3-0 libssh2-1 libssl1.0.2 libtasn1-6 libthai-data libthai0 libtiff5 libtimedate-perl libtool libunistring0 libvecmath-java libvorbis0a libvorbisenc2 libwayland-client0 libwayland-cursor0 libwayland-egl1-mesa libwayland-server0 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 lsb-base m4 man-db mime-support openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless openssl parafly po-debconf python3 python3-minimal python3.5 python3.5-minimal readline-common sbuild-build-depends-trinityrnaseq-dummy shared-mime-info ucf x11-common x11-utils xkb-data 0 upgraded, 222 newly installed, 0 to remove and 0 not upgraded. Need to get 122 MB of archives. After this operation, 421 MB of additional disk space will be used. Get:1 copy:/<>/resolver-W8x41w/apt_archive ./ sbuild-build-depends-trinityrnaseq-dummy 0.invalid.0 [878 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libwrap0 amd64 7.6.q-25 [58.5 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-8 [1162 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.5-1 [1003 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.0-1 [82.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libpng16-16 amd64 1.6.24-2 [279 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libfreetype6 amd64 2.6.3-3+b1 [437 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 ucf all 3.0036 [70.2 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libfontconfig1 amd64 2.11.0-6.7 [331 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig amd64 2.11.0-6.7 [403 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20160629 [27.6 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 x11-common all 1:7.7+16 [251 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libice6 amd64 2:1.0.9-1+b1 [58.8 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libogg0 amd64 1.3.2-1 [19.9 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libsm6 amd64 2:1.2.2-1+b1 [33.6 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [26.2 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1 amd64 1.11.1-1.1 [45.3 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libx11-data all 2:1.6.3-1 [128 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libx11-6 amd64 2:1.6.3-1 [742 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libx11-xcb1 amd64 2:1.6.3-1 [176 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.4-1 [17.4 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libxfixes3 amd64 1:5.0.2-1 [21.3 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libxrender1 amd64 1:0.9.9-2 [31.8 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libxcursor1 amd64 1:1.1.14-1+b1 [35.1 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libxdamage1 amd64 1:1.1.4-2+b1 [14.7 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1 [52.7 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libxft2 amd64 2.3.2-1 [55.4 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libxinerama1 amd64 2:1.1.3-1+b1 [16.9 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libxpm4 amd64 1:3.5.11-1+b1 [48.1 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libxshmfence1 amd64 1.2-1 [7836 B] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libxi6 amd64 2:1.7.6-1 [80.6 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libxtst6 amd64 2:1.2.2-1+b1 [27.3 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libxv1 amd64 2:1.0.10-1+b1 [24.0 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libxxf86dga1 amd64 2:1.1.4-1+b1 [22.3 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1 [20.9 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2h-1 [1287 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 openssl amd64 1.0.2h-1 [681 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 ca-certificates all 20160104 [200 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 java-common all 0.57 [13.4 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 default-jre-headless amd64 2:1.8-57 [10.1 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libnspr4 amd64 2:4.12-6 [117 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.14.1-1 [559 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libnss3 amd64 2:3.26-1 [1158 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 ca-certificates-java all 20160321 [14.4 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libavahi-common-data amd64 0.6.32-1 [118 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libavahi-common3 amd64 0.6.32-1 [52.1 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libdbus-1-3 amd64 1.10.10-1 [190 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libavahi-client3 amd64 0.6.32-1 [55.4 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-5 [111 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.9-4 [50.0 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.3-3 [801 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.14.3+dfsg-1 [61.0 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.14.3+dfsg-1 [115 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.14.3+dfsg-1 [311 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.14.3+dfsg-1 [154 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libcups2 amd64 2.1.4-4 [299 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 liblcms2-2 amd64 2.7-1 [140 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.0-1 [132 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 libpcsclite1 amd64 1.8.18-1 [56.4 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 openjdk-8-jre-headless amd64 8u102-b14.1-2 [26.9 MB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 libpython3.5-minimal amd64 3.5.2-3 [568 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 python3.5-minimal amd64 3.5.2-3 [1644 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 python3-minimal amd64 3.5.1-4 [35.3 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 mime-support all 3.60 [36.7 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libmpdec2 amd64 2.4.2-1 [85.2 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 6.3-8 [57.7 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 libreadline6 amd64 6.3-8+b4 [142 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libpython3.5-stdlib amd64 3.5.2-3 [2126 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 python3.5 amd64 3.5.2-3 [214 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 libpython3-stdlib amd64 3.5.1-4 [18.6 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 dh-python all 2.20160818 [83.0 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 python3 amd64 3.5.1-4 [21.6 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libjbig0 amd64 2.1-3.1 [30.7 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libcap2 amd64 1:2.25-1 [16.8 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 hicolor-icon-theme all 0.15-1 [9550 B] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libtiff5 amd64 4.0.6-2 [222 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 shared-mime-info amd64 1.6-1 [685 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.34.0-1 [309 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libgdk-pixbuf2.0-0 amd64 2.34.0-1 [164 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 gtk-update-icon-cache amd64 3.20.9-1 [73.9 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libpixman-1-0 amd64 0.33.6-1 [532 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-render0 amd64 1.11.1-1.1 [17.5 kB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shm0 amd64 1.11.1-1.1 [11.6 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 libcairo2 amd64 1.14.6-1+b1 [767 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 libthai-data all 0.1.25-1 [165 kB] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 libdatrie1 amd64 0.2.10-2 [35.8 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 libthai0 amd64 0.1.25-1 [51.6 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 libpango-1.0-0 amd64 1.40.1-1 [311 kB] Get:109 http://127.0.0.1:9999/debian unstable/main amd64 libgraphite2-3 amd64 1.3.8-1 [76.4 kB] Get:110 http://127.0.0.1:9999/debian unstable/main amd64 libharfbuzz0b amd64 1.2.7-1+b1 [612 kB] Get:111 http://127.0.0.1:9999/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.40.1-1 [236 kB] Get:112 http://127.0.0.1:9999/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.40.1-1 [223 kB] Get:113 http://127.0.0.1:9999/debian unstable/main amd64 librsvg2-2 amd64 2.40.16-1 [281 kB] Get:114 http://127.0.0.1:9999/debian unstable/main amd64 librsvg2-common amd64 2.40.16-1 [193 kB] Get:115 http://127.0.0.1:9999/debian unstable/main amd64 adwaita-icon-theme all 3.20-3 [11.9 MB] Get:116 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:117 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:118 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:119 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:120 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:121 http://127.0.0.1:9999/debian unstable/main amd64 automake1.11 all 1:1.11.6-3 [537 kB] Get:122 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:123 http://127.0.0.1:9999/debian unstable/main amd64 libdconf1 amd64 0.26.0-1 [37.0 kB] Get:124 http://127.0.0.1:9999/debian unstable/main amd64 dconf-service amd64 0.26.0-1 [42.7 kB] Get:125 http://127.0.0.1:9999/debian unstable/main amd64 dconf-gsettings-backend amd64 0.26.0-1 [35.5 kB] Get:126 http://127.0.0.1:9999/debian unstable/main amd64 dctrl-tools amd64 2.24-2 [101 kB] Get:127 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:128 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:129 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:130 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:131 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:132 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:133 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:134 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:135 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:136 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:137 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:138 http://127.0.0.1:9999/debian unstable/main amd64 libgtk2.0-common all 2.24.30-4 [2691 kB] Get:139 http://127.0.0.1:9999/debian unstable/main amd64 libatk1.0-data all 2.20.0-1 [185 kB] Get:140 http://127.0.0.1:9999/debian unstable/main amd64 libatk1.0-0 amd64 2.20.0-1 [92.9 kB] Get:141 http://127.0.0.1:9999/debian unstable/main amd64 libxrandr2 amd64 2:1.5.0-1 [36.0 kB] Get:142 http://127.0.0.1:9999/debian unstable/main amd64 gnome-icon-theme all 3.12.0-2 [9890 kB] Get:143 http://127.0.0.1:9999/debian unstable/main amd64 libgtk2.0-0 amd64 2.24.30-4 [1802 kB] Get:144 http://127.0.0.1:9999/debian unstable/main amd64 libdrm2 amd64 2.4.70-1 [35.5 kB] Get:145 http://127.0.0.1:9999/debian unstable/main amd64 libglapi-mesa amd64 11.2.2-1 [56.7 kB] Get:146 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-dri2-0 amd64 1.11.1-1.1 [12.9 kB] Get:147 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-dri3-0 amd64 1.11.1-1.1 [11.2 kB] Get:148 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-glx0 amd64 1.11.1-1.1 [27.0 kB] Get:149 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-present0 amd64 1.11.1-1.1 [11.2 kB] Get:150 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-randr0 amd64 1.11.1-1.1 [20.6 kB] Get:151 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shape0 amd64 1.11.1-1.1 [11.7 kB] Get:152 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-sync1 amd64 1.11.1-1.1 [14.4 kB] Get:153 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-xfixes0 amd64 1.11.1-1.1 [14.8 kB] Get:154 http://127.0.0.1:9999/debian unstable/main amd64 libgl1-mesa-glx amd64 11.2.2-1 [162 kB] Get:155 http://127.0.0.1:9999/debian unstable/main amd64 libatspi2.0-0 amd64 2.20.2-1 [60.5 kB] Get:156 http://127.0.0.1:9999/debian unstable/main amd64 libatk-bridge2.0-0 amd64 2.20.1-3 [56.0 kB] Get:157 http://127.0.0.1:9999/debian unstable/main amd64 libcairo-gobject2 amd64 1.14.6-1+b1 [333 kB] Get:158 http://127.0.0.1:9999/debian unstable/main amd64 libgtk-3-common all 3.20.9-1 [3438 kB] Get:159 http://127.0.0.1:9999/debian unstable/main amd64 libcolord2 amd64 1.3.2-1 [250 kB] Get:160 http://127.0.0.1:9999/debian unstable/main amd64 libepoxy0 amd64 1.3.1-1 [175 kB] Get:161 http://127.0.0.1:9999/debian unstable/main amd64 libjson-glib-1.0-common all 1.2.2-1 [161 kB] Get:162 http://127.0.0.1:9999/debian unstable/main amd64 libjson-glib-1.0-0 amd64 1.2.2-1 [173 kB] Get:163 http://127.0.0.1:9999/debian unstable/main amd64 libproxy1v5 amd64 0.4.11-5 [54.5 kB] Get:164 http://127.0.0.1:9999/debian unstable/main amd64 glib-networking-common all 2.48.2-1 [56.9 kB] Get:165 http://127.0.0.1:9999/debian unstable/main amd64 glib-networking-services amd64 2.48.2-1 [19.7 kB] Get:166 http://127.0.0.1:9999/debian unstable/main amd64 gsettings-desktop-schemas all 3.20.0-3 [450 kB] Get:167 http://127.0.0.1:9999/debian unstable/main amd64 glib-networking amd64 2.48.2-1 [56.8 kB] Get:168 http://127.0.0.1:9999/debian unstable/main amd64 libsoup2.4-1 amd64 2.54.1-1 [283 kB] Get:169 http://127.0.0.1:9999/debian unstable/main amd64 libsoup-gnome2.4-1 amd64 2.54.1-1 [61.0 kB] Get:170 http://127.0.0.1:9999/debian unstable/main amd64 librest-0.7-0 amd64 0.8.0-1 [32.9 kB] Get:171 http://127.0.0.1:9999/debian unstable/main amd64 libwayland-client0 amd64 1.11.0-2 [24.7 kB] Get:172 http://127.0.0.1:9999/debian unstable/main amd64 libwayland-cursor0 amd64 1.11.0-2 [13.1 kB] Get:173 http://127.0.0.1:9999/debian unstable/main amd64 libwayland-server0 amd64 1.11.0-2 [29.6 kB] Get:174 http://127.0.0.1:9999/debian unstable/main amd64 libgbm1 amd64 11.2.2-1 [57.9 kB] Get:175 http://127.0.0.1:9999/debian unstable/main amd64 libegl1-mesa amd64 11.2.2-1 [106 kB] Get:176 http://127.0.0.1:9999/debian unstable/main amd64 libwayland-egl1-mesa amd64 11.2.2-1 [40.8 kB] Get:177 http://127.0.0.1:9999/debian unstable/main amd64 xkb-data all 2.17-1 [627 kB] Get:178 http://127.0.0.1:9999/debian unstable/main amd64 libxkbcommon0 amd64 0.6.1-1 [121 kB] Get:179 http://127.0.0.1:9999/debian unstable/main amd64 libgtk-3-0 amd64 3.20.9-1 [2423 kB] Get:180 http://127.0.0.1:9999/debian unstable/main amd64 libfontenc1 amd64 1:1.1.3-1 [24.1 kB] Get:181 http://127.0.0.1:9999/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:182 http://127.0.0.1:9999/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:183 http://127.0.0.1:9999/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1 [200 kB] Get:184 http://127.0.0.1:9999/debian unstable/main amd64 libxmuu1 amd64 2:1.1.2-2 [23.5 kB] Get:185 http://127.0.0.1:9999/debian unstable/main amd64 x11-utils amd64 7.7+3 [193 kB] Get:186 http://127.0.0.1:9999/debian unstable/main amd64 libatk-wrapper-java all 0.33.3-8 [43.7 kB] Get:187 http://127.0.0.1:9999/debian unstable/main amd64 libatk-wrapper-java-jni amd64 0.33.3-8 [36.8 kB] Get:188 http://127.0.0.1:9999/debian unstable/main amd64 libasound2-data all 1.1.2-1 [207 kB] Get:189 http://127.0.0.1:9999/debian unstable/main amd64 libasound2 amd64 1.1.2-1 [535 kB] Get:190 http://127.0.0.1:9999/debian unstable/main amd64 libgif7 amd64 5.1.4-0.3 [42.8 kB] Get:191 http://127.0.0.1:9999/debian unstable/main amd64 libasyncns0 amd64 0.8-6 [12.5 kB] Get:192 http://127.0.0.1:9999/debian unstable/main amd64 libjson-c3 amd64 0.12-3 [25.5 kB] Get:193 http://127.0.0.1:9999/debian unstable/main amd64 libflac8 amd64 1.3.1-4 [218 kB] Get:194 http://127.0.0.1:9999/debian unstable/main amd64 libvorbis0a amd64 1.3.5-3 [92.9 kB] Get:195 http://127.0.0.1:9999/debian unstable/main amd64 libvorbisenc2 amd64 1.3.5-3 [78.9 kB] Get:196 http://127.0.0.1:9999/debian unstable/main amd64 libsndfile1 amd64 1.0.25-10 [214 kB] Get:197 http://127.0.0.1:9999/debian unstable/main amd64 libpulse0 amd64 9.0-2 [272 kB] Get:198 http://127.0.0.1:9999/debian unstable/main amd64 openjdk-8-jre amd64 8u102-b14.1-2 [69.6 kB] Get:199 http://127.0.0.1:9999/debian unstable/main amd64 default-jre amd64 2:1.8-57 [934 B] Get:200 http://127.0.0.1:9999/debian unstable/main amd64 openjdk-8-jdk-headless amd64 8u102-b14.1-2 [8117 kB] Get:201 http://127.0.0.1:9999/debian unstable/main amd64 default-jdk-headless amd64 2:1.8-57 [940 B] Get:202 http://127.0.0.1:9999/debian unstable/main amd64 openjdk-8-jdk amd64 8u102-b14.1-2 [430 kB] Get:203 http://127.0.0.1:9999/debian unstable/main amd64 default-jdk amd64 2:1.8-57 [928 B] Get:204 http://127.0.0.1:9999/debian unstable/main amd64 devscripts amd64 2.16.7 [925 kB] Get:205 http://127.0.0.1:9999/debian unstable/main amd64 jaligner all 1.0+dfsg-4 [128 kB] Get:206 http://127.0.0.1:9999/debian unstable/main amd64 javahelper all 0.58 [84.9 kB] Get:207 http://127.0.0.1:9999/debian unstable/main amd64 libjellyfish-2.0-2 amd64 2.2.5-1 [62.5 kB] Get:208 http://127.0.0.1:9999/debian unstable/main amd64 jellyfish amd64 2.2.5-1 [348 kB] Get:209 http://127.0.0.1:9999/debian unstable/main amd64 libconcurrent-java all 1.3.4-4 [133 kB] Get:210 http://127.0.0.1:9999/debian unstable/main amd64 libcolt-free-java all 1.2.0+dfsg-4 [405 kB] Get:211 http://127.0.0.1:9999/debian unstable/main amd64 libcommons-collections4-java all 4.1-1 [656 kB] Get:212 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.13.0-1 [79.4 kB] Get:213 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [60.0 kB] Get:214 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB] Get:215 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.50.1-1 [278 kB] Get:216 http://127.0.0.1:9999/debian unstable/main amd64 libgetopt-java all 1.0.14+dfsg-3 [24.9 kB] Get:217 http://127.0.0.1:9999/debian unstable/main amd64 libhts1 amd64 1.3.1-2 [256 kB] Get:218 http://127.0.0.1:9999/debian unstable/main amd64 libhts-dev amd64 1.3.1-2 [315 kB] Get:219 http://127.0.0.1:9999/debian unstable/main amd64 libjs-jquery all 1.12.4-1 [167 kB] Get:220 http://127.0.0.1:9999/debian unstable/main amd64 libvecmath-java all 1.5.2-5 [76.9 kB] Get:221 http://127.0.0.1:9999/debian unstable/main amd64 libjung-free-java all 2.0.1+dfsg-1 [976 kB] Get:222 http://127.0.0.1:9999/debian unstable/main amd64 parafly amd64 0.0.2013.01.21-3 [15.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 122 MB in 1s (70.3 MB/s) Selecting previously unselected package libwrap0:amd64. (Reading database ... 9775 files and directories currently installed.) Preparing to unpack .../00-libwrap0_7.6.q-25_amd64.deb ... Unpacking libwrap0:amd64 (7.6.q-25) ... Selecting previously unselected package groff-base. Preparing to unpack .../01-groff-base_1.22.3-8_amd64.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.10_amd64.deb ... Unpacking bsdmainutils (9.0.10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.5-1_amd64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../05-libexpat1_2.2.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../06-libpng16-16_1.6.24-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.24-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../07-libfreetype6_2.6.3-3+b1_amd64.deb ... Unpacking libfreetype6:amd64 (2.6.3-3+b1) ... Selecting previously unselected package ucf. Preparing to unpack .../08-ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../09-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../10-fontconfig-config_2.11.0-6.7_all.deb ... Unpacking fontconfig-config (2.11.0-6.7) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../11-libfontconfig1_2.11.0-6.7_amd64.deb ... Unpacking libfontconfig1:amd64 (2.11.0-6.7) ... Selecting previously unselected package fontconfig. Preparing to unpack .../12-fontconfig_2.11.0-6.7_amd64.deb ... Unpacking fontconfig (2.11.0-6.7) ... Selecting previously unselected package lsb-base. Preparing to unpack .../13-lsb-base_9.20160629_all.deb ... Unpacking lsb-base (9.20160629) ... Selecting previously unselected package x11-common. Preparing to unpack .../14-x11-common_1%3a7.7+16_all.deb ... Unpacking x11-common (1:7.7+16) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../15-libice6_2%3a1.0.9-1+b1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.9-1+b1) ... Selecting previously unselected package libogg0:amd64. Preparing to unpack .../16-libogg0_1.3.2-1_amd64.deb ... Unpacking libogg0:amd64 (1.3.2-1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../17-libsm6_2%3a1.2.2-1+b1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.2-1+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../18-libxau6_1%3a1.0.8-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../19-libxdmcp6_1%3a1.1.2-1.1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-1.1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../20-libxcb1_1.11.1-1.1_amd64.deb ... Unpacking libxcb1:amd64 (1.11.1-1.1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../21-libx11-data_2%3a1.6.3-1_all.deb ... Unpacking libx11-data (2:1.6.3-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../22-libx11-6_2%3a1.6.3-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.3-1) ... Selecting previously unselected package libx11-xcb1:amd64. Preparing to unpack .../23-libx11-xcb1_2%3a1.6.3-1_amd64.deb ... Unpacking libx11-xcb1:amd64 (2:1.6.3-1) ... Selecting previously unselected package libxcomposite1:amd64. Preparing to unpack .../24-libxcomposite1_1%3a0.4.4-1_amd64.deb ... Unpacking libxcomposite1:amd64 (1:0.4.4-1) ... Selecting previously unselected package libxfixes3:amd64. Preparing to unpack .../25-libxfixes3_1%3a5.0.2-1_amd64.deb ... Unpacking libxfixes3:amd64 (1:5.0.2-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../26-libxrender1_1%3a0.9.9-2_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.9-2) ... Selecting previously unselected package libxcursor1:amd64. Preparing to unpack .../27-libxcursor1_1%3a1.1.14-1+b1_amd64.deb ... Unpacking libxcursor1:amd64 (1:1.1.14-1+b1) ... Selecting previously unselected package libxdamage1:amd64. Preparing to unpack .../28-libxdamage1_1%3a1.1.4-2+b1_amd64.deb ... Unpacking libxdamage1:amd64 (1:1.1.4-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../29-libxext6_2%3a1.3.3-1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../30-libxft2_2.3.2-1_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-1) ... Selecting previously unselected package libxinerama1:amd64. Preparing to unpack .../31-libxinerama1_2%3a1.1.3-1+b1_amd64.deb ... Unpacking libxinerama1:amd64 (2:1.1.3-1+b1) ... Selecting previously unselected package libxpm4:amd64. Preparing to unpack .../32-libxpm4_1%3a3.5.11-1+b1_amd64.deb ... Unpacking libxpm4:amd64 (1:3.5.11-1+b1) ... Selecting previously unselected package libxshmfence1:amd64. Preparing to unpack .../33-libxshmfence1_1.2-1_amd64.deb ... Unpacking libxshmfence1:amd64 (1.2-1) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../34-libxi6_2%3a1.7.6-1_amd64.deb ... Unpacking libxi6:amd64 (2:1.7.6-1) ... Selecting previously unselected package libxtst6:amd64. Preparing to unpack .../35-libxtst6_2%3a1.2.2-1+b1_amd64.deb ... Unpacking libxtst6:amd64 (2:1.2.2-1+b1) ... Selecting previously unselected package libxv1:amd64. Preparing to unpack .../36-libxv1_2%3a1.0.10-1+b1_amd64.deb ... Unpacking libxv1:amd64 (2:1.0.10-1+b1) ... Selecting previously unselected package libxxf86dga1:amd64. Preparing to unpack .../37-libxxf86dga1_2%3a1.1.4-1+b1_amd64.deb ... Unpacking libxxf86dga1:amd64 (2:1.1.4-1+b1) ... Selecting previously unselected package libxxf86vm1:amd64. Preparing to unpack .../38-libxxf86vm1_1%3a1.1.4-1_amd64.deb ... Unpacking libxxf86vm1:amd64 (1:1.1.4-1) ... Selecting previously unselected package libssl1.0.2:amd64. Preparing to unpack .../39-libssl1.0.2_1.0.2h-1_amd64.deb ... Unpacking libssl1.0.2:amd64 (1.0.2h-1) ... Selecting previously unselected package openssl. Preparing to unpack .../40-openssl_1.0.2h-1_amd64.deb ... Unpacking openssl (1.0.2h-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../41-ca-certificates_20160104_all.deb ... Unpacking ca-certificates (20160104) ... Selecting previously unselected package java-common. Preparing to unpack .../42-java-common_0.57_all.deb ... Unpacking java-common (0.57) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../43-default-jre-headless_2%3a1.8-57_amd64.deb ... Unpacking default-jre-headless (2:1.8-57) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../44-libnspr4_2%3a4.12-6_amd64.deb ... Unpacking libnspr4:amd64 (2:4.12-6) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../45-libsqlite3-0_3.14.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.14.1-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../46-libnss3_2%3a3.26-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.26-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../47-ca-certificates-java_20160321_all.deb ... Unpacking ca-certificates-java (20160321) ... Selecting previously unselected package libavahi-common-data:amd64. 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Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.10) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libvorbis0a:amd64 (1.3.5-3) ... Setting up x11-common (1:7.7+16) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up ca-certificates (20160104) ... Setting up hicolor-icon-theme (0.15-1) ... Setting up libgetopt-java (1.0.14+dfsg-3) ... Setting up libwayland-cursor0:amd64 (1.11.0-2) ... Setting up libx11-data (2:1.6.3-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-1) ... Setting up libidn11:amd64 (1.33-1) ... Setting up libjellyfish-2.0-2 (2.2.5-1) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up libdbus-1-3:amd64 (1.10.10-1) ... Setting up libreadline6:amd64 (6.3-8+b4) ... Setting up libwrap0:amd64 (7.6.q-25) ... Setting up libavahi-common-data:amd64 (0.6.32-1) ... Setting up libwayland-server0:amd64 (1.11.0-2) ... Setting up libfile-stripnondeterminism-perl (0.023-2) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up dconf-service (0.26.0-1) ... Setting up gettext (0.19.8.1-1) ... Setting up libpython3.5-stdlib:amd64 (3.5.2-3) ... Setting up libgbm1:amd64 (11.2.2-1) ... Setting up libgnutls30:amd64 (3.5.3-3) ... Setting up libflac8:amd64 (1.3.1-4) ... Setting up libnss3:amd64 (2:3.26-1) ... Setting up libharfbuzz0b:amd64 (1.2.7-1+b1) ... Setting up autoconf (2.69-10) ... Setting up libthai0:amd64 (0.1.25-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ... Setting up file (1:5.28-4) ... Setting up libkrb5support0:amd64 (1.14.3+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ... Setting up jellyfish (2.2.5-1) ... Setting up automake (1:1.15-4) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:amd64 (2:1.0.9-1+b1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libavahi-common3:amd64 (0.6.32-1) ... Setting up libvorbisenc2:amd64 (1.3.5-3) ... Setting up dconf-gsettings-backend:amd64 (0.26.0-1) ... Setting up libxcb1:amd64 (1.11.1-1.1) ... Setting up automake1.11 (1:1.11.6-3) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.2-3) ... Setting up libpython3-stdlib:amd64 (3.5.1-4) ... Setting up libxcb-present0:amd64 (1.11.1-1.1) ... Setting up libfontconfig1:amd64 (2.11.0-6.7) ... Setting up libxcb-dri2-0:amd64 (1.11.1-1.1) ... Setting up libsm6:amd64 (2:1.2.2-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.11.1-1.1) ... Setting up libk5crypto3:amd64 (1.14.3+dfsg-1) ... Setting up libxcb-glx0:amd64 (1.11.1-1.1) ... Setting up libxcb-randr0:amd64 (1.11.1-1.1) ... Setting up libxcb-xfixes0:amd64 (1.11.1-1.1) ... Setting up libxcb-render0:amd64 (1.11.1-1.1) ... Setting up po-debconf (1.0.19) ... Setting up gsettings-desktop-schemas (3.20.0-3) ... Setting up libgtk-3-common (3.20.9-1) ... Setting up libx11-6:amd64 (2:1.6.3-1) ... Setting up libxmuu1:amd64 (2:1.1.2-2) ... Setting up libxcb-sync1:amd64 (1.11.1-1.1) ... Setting up libsndfile1:amd64 (1.0.25-10) ... Setting up libx11-xcb1:amd64 (2:1.6.3-1) ... Setting up glib-networking:amd64 (2.48.2-1) ... Setting up libxcomposite1:amd64 (1:0.4.4-1) ... Setting up libxcb-shm0:amd64 (1.11.1-1.1) ... Setting up libxpm4:amd64 (1:3.5.11-1+b1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxcb-shape0:amd64 (1.11.1-1.1) ... Setting up libxrender1:amd64 (1:0.9.9-2) ... Setting up libavahi-client3:amd64 (0.6.32-1) ... Setting up libkrb5-3:amd64 (1.14.3+dfsg-1) ... Setting up libxft2:amd64 (2.3.2-1) ... Setting up fontconfig (2.11.0-6.7) ... Regenerating fonts cache... done. Setting up libegl1-mesa:amd64 (11.2.2-1) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxfixes3:amd64 (1:5.0.2-1) ... Setting up libatspi2.0-0:amd64 (2.20.2-1) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.34.0-1) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.14.3+dfsg-1) ... Setting up gtk-update-icon-cache (3.20.9-1) ... Setting up libxcursor1:amd64 (1:1.1.14-1+b1) ... Setting up libxxf86dga1:amd64 (2:1.1.4-1+b1) ... Setting up libpango-1.0-0:amd64 (1.40.1-1) ... Setting up libwayland-egl1-mesa:amd64 (11.2.2-1) ... Setting up libatk-bridge2.0-0:amd64 (2.20.1-3) ... Setting up libxv1:amd64 (2:1.0.10-1+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1) ... Setting up libxrandr2:amd64 (2:1.5.0-1) ... Setting up libcups2:amd64 (2.1.4-4) ... Setting up libxi6:amd64 (2:1.7.6-1) ... Setting up libxaw7:amd64 (2:1.0.13-1) ... Setting up libcairo2:amd64 (1.14.6-1+b1) ... Setting up libxinerama1:amd64 (2:1.1.3-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.4-2+b1) ... Setting up libcurl3-gnutls:amd64 (7.50.1-1) ... Setting up libcairo-gobject2:amd64 (1.14.6-1+b1) ... Setting up libsoup2.4-1:amd64 (2.54.1-1) ... Setting up libsoup-gnome2.4-1:amd64 (2.54.1-1) ... Setting up libxtst6:amd64 (2:1.2.2-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.1-1) ... Setting up libgl1-mesa-glx:amd64 (11.2.2-1) ... Setting up librest-0.7-0:amd64 (0.8.0-1) ... Setting up libhts1:amd64 (1.3.1-2) ... Setting up libhts-dev:amd64 (1.3.1-2) ... Setting up x11-utils (7.7+3) ... Setting up libpangocairo-1.0-0:amd64 (1.40.1-1) ... Setting up libpulse0:amd64 (9.0-2) ... Setting up libatk-wrapper-java (0.33.3-8) ... Setting up librsvg2-2:amd64 (2.40.16-1) ... Setting up librsvg2-common:amd64 (2.40.16-1) ... Setting up adwaita-icon-theme (3.20-3) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libgtk2.0-0:amd64 (2.24.30-4) ... Setting up gnome-icon-theme (3.12.0-2) ... update-alternatives: using /usr/share/icons/gnome/scalable/places/debian-swirl.svg to provide /usr/share/icons/gnome/scalable/places/start-here.svg (start-here.svg) in auto mode Setting up libgtk-3-0:amd64 (3.20.9-1) ... Setting up libatk-wrapper-java-jni:amd64 (0.33.3-8) ... Setting up dh-python (2.20160818) ... Setting up openjdk-8-jre-headless:amd64 (8u102-b14.1-2) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libconcurrent-java (1.3.4-4) ... Setting up ca-certificates-java (20160321) ... done. Setting up dh-autoreconf (12) ... Setting up python3 (3.5.1-4) ... Setting up openjdk-8-jdk-headless:amd64 (8u102-b14.1-2) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode Setting up devscripts (2.16.7) ... Setting up dh-strip-nondeterminism (0.023-2) ... Setting up openjdk-8-jre:amd64 (8u102-b14.1-2) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up libcolt-free-java (1.2.0+dfsg-4) ... Setting up default-jre-headless (2:1.8-57) ... Setting up default-jdk-headless (2:1.8-57) ... Setting up libjung-free-java (2.0.1+dfsg-1) ... Setting up debhelper (9.20160814) ... Setting up openjdk-8-jdk:amd64 (8u102-b14.1-2) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jre (2:1.8-57) ... Setting up jaligner (1.0+dfsg-4) ... Setting up javahelper (0.58) ... Setting up default-jdk (2:1.8-57) ... Setting up sbuild-build-depends-trinityrnaseq-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-5) ... Processing triggers for ca-certificates (20160104) ... Updating certificates in /etc/ssl/certs... 173 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... Adding debian:ACCVRAIZ1.pem Adding debian:ACEDICOM_Root.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CA_WoSign_ECC_Root.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CNNIC_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:Certification_Authority_of_WoSign_G2.pem Adding debian:Certigna.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Certum_Root_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:ComSign_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:EC-ACC.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Equifax_Secure_CA.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:IGC_A.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Juur-SK.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:PSCProcert.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:S-TRUST_Universal_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:StartCom_Certification_Authority_2.pem Adding debian:StartCom_Certification_Authority_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Taiwan_GRCA.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:WoSign.pem Adding debian:WoSign_China.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem done. done. Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.34.0-1) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.27-6 dpkg-dev_1.18.10 g++-6_6.2.0-1 gcc-6_6.2.0-1 libc6-dev_2.23-5 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 linux-libc-dev_4.7.2-1 Package versions: adduser_3.115 adwaita-icon-theme_3.20-3 apt_1.3~rc2 autoconf_2.69-10 automake_1:1.15-4 automake1.11_1:1.11.6-3 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6 base-passwd_3.5.40 bash_4.3-15 binutils_2.27-6 bsdmainutils_9.0.10 bsdutils_1:2.28.1-1 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20160104 ca-certificates-java_20160321 clang-3.8_1:3.8.1-9 coreutils_8.25-2 cpp_4:6.1.1-1 cpp-6_6.2.0-1 dash_0.5.8-2.3 dconf-gsettings-backend_0.26.0-1 dconf-service_0.26.0-1 dctrl-tools_2.24-2 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debian-archive-keyring_2014.3 debianutils_4.8 default-jdk_2:1.8-57 default-jdk-headless_2:1.8-57 default-jre_2:1.8-57 default-jre-headless_2:1.8-57 devscripts_2.16.7 dh-autoreconf_12 dh-python_2.20160818 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 eatmydata_105-3 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 g++_4:6.1.1-1 g++-6_6.2.0-1 gcc_4:6.1.1-1 gcc-6_6.2.0-1 gcc-6-base_6.2.0-1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 glib-networking_2.48.2-1 glib-networking-common_2.48.2-1 glib-networking-services_2.48.2-1 gnome-icon-theme_3.12.0-2 gpgv_2.1.14-5 grep_2.25-6 groff-base_1.22.3-8 gsettings-desktop-schemas_3.20.0-3 gtk-update-icon-cache_3.20.9-1 gzip_1.6-5 hicolor-icon-theme_0.15-1 hostname_3.18 init-system-helpers_1.42 intltool-debian_0.35.0+20060710.4 jaligner_1.0+dfsg-4 java-common_0.57 javahelper_0.58 jellyfish_2.2.5-1 libacl1_2.2.52-3 libapt-pkg5.0_1.3~rc2 libarchive-zip-perl_1.59-1 libasan3_6.2.0-1 libasound2_1.1.2-1 libasound2-data_1.1.2-1 libasyncns0_0.8-6 libatk-bridge2.0-0_2.20.1-3 libatk-wrapper-java_0.33.3-8 libatk-wrapper-java-jni_0.33.3-8 libatk1.0-0_2.20.0-1 libatk1.0-data_2.20.0-1 libatomic1_6.2.0-1 libatspi2.0-0_2.20.2-1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libavahi-client3_0.6.32-1 libavahi-common-data_0.6.32-1 libavahi-common3_0.6.32-1 libblkid1_2.28.1-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-5 libc-dev-bin_2.23-5 libc6_2.23-5 libc6-dev_2.23-5 libcairo-gobject2_1.14.6-1+b1 libcairo2_1.14.6-1+b1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.2.0-1 libcilkrts5_6.2.0-1 libclang-common-3.8-dev_1:3.8.1-9 libclang1-3.8_1:3.8.1-9 libcolord2_1.3.2-1 libcolt-free-java_1.2.0+dfsg-4 libcomerr2_1.43.1-1 libcommons-collections4-java_4.1-1 libconcurrent-java_1.3.4-4 libcroco3_0.6.11-1 libcups2_2.1.4-4 libcurl3-gnutls_7.50.1-1 libdatrie1_0.2.10-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.10-1 libdconf1_0.26.0-1 libdebconfclient0_0.215 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libeatmydata1_105-3 libedit2_3.1-20150325-1+b1 libegl1-mesa_11.2.2-1 libepoxy0_1.3.1-1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libflac8_1.3.1-4 libfontconfig1_2.11.0-6.7 libfontenc1_1:1.1.3-1 libfreetype6_2.6.3-3+b1 libgbm1_11.2.2-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-1 libgcc1_1:6.2.0-1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libgdk-pixbuf2.0-0_2.34.0-1 libgdk-pixbuf2.0-common_2.34.0-1 libgetopt-java_1.0.14+dfsg-3 libgif7_5.1.4-0.3 libgl1-mesa-glx_11.2.2-1 libglapi-mesa_11.2.2-1 libglib2.0-0_2.48.1-3 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-3 libgomp1_6.2.0-1 libgpg-error0_1.24-1 libgraphite2-3_1.3.8-1 libgssapi-krb5-2_1.14.3+dfsg-1 libgtk-3-0_3.20.9-1 libgtk-3-common_3.20.9-1 libgtk2.0-0_2.24.30-4 libgtk2.0-common_2.24.30-4 libharfbuzz0b_1.2.7-1+b1 libhogweed4_3.2-1 libhts-dev_1.3.1-2 libhts1_1.3.1-2 libice6_2:1.0.9-1+b1 libicu57_57.1-3 libidn11_1.33-1 libisl15_0.17.1-1 libitm1_6.2.0-1 libjbig0_2.1-3.1 libjellyfish-2.0-2_2.2.5-1 libjpeg62-turbo_1:1.5.0-1 libjs-jquery_1.12.4-1 libjson-c3_0.12-3 libjson-glib-1.0-0_1.2.2-1 libjson-glib-1.0-common_1.2.2-1 libjung-free-java_2.0.1+dfsg-1 libk5crypto3_1.14.3+dfsg-1 libkeyutils1_1.5.9-9 libkrb5-3_1.14.3+dfsg-1 libkrb5support0_1.14.3+dfsg-1 liblcms2-2_2.7-1 libldap-2.4-2_2.4.42+dfsg-2+b2 libllvm3.8_1:3.8.1-9 liblsan0_6.2.0-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.1-1 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-2 libmpx2_6.2.0-1 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libnettle6_3.2-1 libnghttp2-14_1.13.0-1 libnspr4_2:4.12-6 libnss3_2:3.26-1 libobjc-6-dev_6.2.0-1 libobjc4_6.2.0-1 libogg0_1.3.2-1 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpango-1.0-0_1.40.1-1 libpangocairo-1.0-0_1.40.1-1 libpangoft2-1.0-0_1.40.1-1 libpcre3_2:8.39-2 libpcsclite1_1.8.18-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpng16-16_1.6.24-2 libproxy1v5_0.4.11-5 libpulse0_9.0-2 libpython3-stdlib_3.5.1-4 libpython3.5-minimal_3.5.2-3 libpython3.5-stdlib_3.5.2-3 libquadmath0_6.2.0-1 libreadline6_6.3-8+b4 librest-0.7-0_0.8.0-1 librsvg2-2_2.40.16-1 librsvg2-common_2.40.16-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28.1-1 libsndfile1_1.0.25-10 libsoup-gnome2.4-1_2.54.1-1 libsoup2.4-1_2.54.1-1 libsqlite3-0_3.14.1-1 libss2_1.43.1-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2h-1 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 libsystemd0_231-5 libtasn1-6_4.9-4 libthai-data_0.1.25-1 libthai0_0.1.25-1 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libtsan0_6.2.0-1 libubsan0_6.2.0-1 libudev1_231-5 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-5 libuuid1_2.28.1-1 libvecmath-java_1.5.2-5 libvorbis0a_1.3.5-3 libvorbisenc2_1.3.5-3 libwayland-client0_1.11.0-2 libwayland-cursor0_1.11.0-2 libwayland-egl1-mesa_11.2.2-1 libwayland-server0_1.11.0-2 libwrap0_7.6.q-25 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-xcb1_2:1.6.3-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-dri2-0_1.11.1-1.1 libxcb-dri3-0_1.11.1-1.1 libxcb-glx0_1.11.1-1.1 libxcb-present0_1.11.1-1.1 libxcb-randr0_1.11.1-1.1 libxcb-render0_1.11.1-1.1 libxcb-shape0_1.11.1-1.1 libxcb-shm0_1.11.1-1.1 libxcb-sync1_1.11.1-1.1 libxcb-xfixes0_1.11.1-1.1 libxcb1_1.11.1-1.1 libxcomposite1_1:0.4.4-1 libxcursor1_1:1.1.14-1+b1 libxdamage1_1:1.1.4-2+b1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxfixes3_1:5.0.2-1 libxft2_2.3.2-1 libxi6_2:1.7.6-1 libxinerama1_2:1.1.3-1+b1 libxkbcommon0_0.6.1-1 libxml2_2.9.4+dfsg1-1+b1 libxmu6_2:1.1.2-2 libxmuu1_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrandr2_2:1.5.0-1 libxrender1_1:0.9.9-2 libxshmfence1_1.2-1 libxt6_1:1.1.5-1 libxtst6_2:1.2.2-1+b1 libxv1_2:1.0.10-1+b1 libxxf86dga1_2:1.1.4-1+b1 libxxf86vm1_1:1.1.4-1 linux-libc-dev_4.7.2-1 login_1:4.2-3.1 lsb-base_9.20160629 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28.1-1 multiarch-support_2.23-5 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 openjdk-8-jdk_8u102-b14.1-2 openjdk-8-jdk-headless_8u102-b14.1-2 openjdk-8-jre_8u102-b14.1-2 openjdk-8-jre-headless_8u102-b14.1-2 openssl_1.0.2h-1 parafly_0.0.2013.01.21-3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 python3_3.5.1-4 python3-minimal_3.5.1-4 python3.5_3.5.2-3 python3.5-minimal_3.5.2-3 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-trinityrnaseq-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 shared-mime-info_1.6-1 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 ucf_3.0036 util-linux_2.28.1-1 x11-common_1:7.7+16 x11-utils_7.7+3 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Aug 5 19:36:09 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./trinityrnaseq_2.2.0+dfsg-2.dsc dpkg-source: info: extracting trinityrnaseq in /<>/trinityrnaseq-2.2.0+dfsg dpkg-source: info: unpacking trinityrnaseq_2.2.0+dfsg.orig.tar.xz dpkg-source: info: unpacking trinityrnaseq_2.2.0+dfsg-2.debian.tar.xz dpkg-source: info: applying skip-kallisto-deseq2-tests dpkg-source: info: applying noExitTester dpkg-source: info: applying jellyfish-path dpkg-source: info: applying update-paths dpkg-source: info: applying collections15-to-4 dpkg-source: info: applying 0002-fix_istream_failure_call.patch dpkg-source: info: applying fix_system_paths dpkg-source: info: applying disable-version-check dpkg-source: info: applying adjust-trimmomatic-adapters-path dpkg-source: info: applying build_with_gcc6.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-34ed862d-57f4-4735-a6c4-f5f75011e659 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package trinityrnaseq dpkg-buildpackage: info: source version 2.2.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build trinityrnaseq-2.2.0+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --parallel --with javahelper,autoreconf dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs; do dh_auto_clean \ --sourcedirectory=${target}; done make -j1 clean make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Chrysalis' Makefile:80: ---------------------------------------------------------- Makefile:81: using g++ version 4.2.1 Makefile:82: -------------------------------------------------------- clang: error: unknown argument: '-fno-nonansi-builtins' make[2]: *** [MakeDepend] Error 1 for file in ; do rm -f ./$file; done rm -f MakeDepend ./MakeDepend contigs.out my.permanent.log.file \ core a.out Makefile.bak bsubin BasevectorTables.h ./checkLock find obj -name '*.o' -exec rm {} \; || /bin/true find: 'obj': No such file or directory rm -rf cxx_repository rm -f lib_*_temp.a make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Chrysalis' make -j1 clean make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' rm -f *.o fastool make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' make -j1 clean make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make clean; done <<< src >>> make[3]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src' rm -f slcluster.o graph.o graphnode.o cmd_line_opts.o core a.out *~ \#* slclust Makefile.bak \ ../bin/slclust make[3]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust' make -j1 clean make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/scaffold_iworm_contigs' rm -f scaffold_iworm_contigs make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/scaffold_iworm_contigs' rm --force Chrysalis/Makefile_auto rm --force trinity-plugins/slclust/bin/slclust make[1]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg' jh_clean dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --parallel --with javahelper,autoreconf dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_autoreconf -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs; do dh_auto_configure \ --sourcedirectory=${target} -- \ --prefix=/usr/lib/trinityrnaseq/${target} \ CFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" FCFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong" FFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong" GCJFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong" LDFLAGS="-Wl,-z,relro -Wl,-z,now" OBJCFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" OBJCXXFLAGS="-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" ; done ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --prefix=/usr/lib/trinityrnaseq/Inchworm "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" "FCFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong" "FFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong" "GCJFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" "OBJCFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" "OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for library containing cos... none required checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg' jh_linkjars -a -O--parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs; do dh_auto_build \ -O--sourcedirectory=${target}; done make -j1 make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm' make all-recursive make[3]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm' Making all in src make[4]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Fasta_entry.o Fasta_entry.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IRKE_run.o IRKE_run.cpp IRKE_run.cpp:9:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. Makefile:431: recipe for target 'IRKE_run.o' failed make[4]: *** [IRKE_run.o] Error 1 make[4]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm/src' Makefile:349: recipe for target 'all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm' Makefile:290: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm' dh_auto_build: make -j1 returned exit code 2 make -j1 make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Chrysalis' Makefile:80: ---------------------------------------------------------- Makefile:81: using g++ version 4.2.1 Makefile:82: -------------------------------------------------------- clang: error: unknown argument: '-fno-nonansi-builtins' make[2]: *** [MakeDepend] Error 1 make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Chrysalis' make -j1 make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' cc -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c99 -Werror -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now fastool.c -o fastool make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' make -j1 make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make all; done <<< src >>> make[3]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src' g++ -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o slcluster.o slcluster.cpp In file included from slcluster.cpp:4: ../include/cmd_line_opts.h:1:9: warning: '__CMD_LINE_OPTS_H__' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef __CMD_LINE_OPTS_H__ ^~~~~~~~~~~~~~~~~~~ ../include/cmd_line_opts.h:2:9: note: '__CMD_LiNE_OPTS_H__' is defined here; did you mean '__CMD_LINE_OPTS_H__'? #define __CMD_LiNE_OPTS_H__ ^~~~~~~~~~~~~~~~~~~ __CMD_LINE_OPTS_H__ 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o graph.o graph.cpp g++ -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o graphnode.o graphnode.cpp g++ -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cmd_line_opts.o cmd_line_opts.cpp In file included from cmd_line_opts.cpp:1: ../include/cmd_line_opts.h:1:9: warning: '__CMD_LINE_OPTS_H__' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef __CMD_LINE_OPTS_H__ ^~~~~~~~~~~~~~~~~~~ ../include/cmd_line_opts.h:2:9: note: '__CMD_LiNE_OPTS_H__' is defined here; did you mean '__CMD_LINE_OPTS_H__'? #define __CMD_LiNE_OPTS_H__ ^~~~~~~~~~~~~~~~~~~ __CMD_LINE_OPTS_H__ 1 warning generated. g++ -Wl,-z,relro -Wl,-z,now slcluster.o graph.o graphnode.o cmd_line_opts.o -o slclust chmod 755 slclust make[3]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust' make -j1 make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/scaffold_iworm_contigs' g++ -Wl,-z,relro -Wl,-z,now -I../htslib -L../htslib ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/scaffold_iworm_contigs' make[1]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg' jh_build -a -O--parallel find Butterfly/src/src -name *.java -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javac -g -cp /usr/share/java/commons-collections4.jar:/usr/share/java/gnu-getopt.jar:/usr/share/java/jung-algorithms.jar:/usr/share/java/jung-api.jar:/usr/share/java/jung-graph-impl.jar:/usr/share/java/jaligner.jar:debian/_jh_build.Butterfly -d debian/_jh_build.Butterfly -source 1.5 -target 1.5 warning: [options] bootstrap class path not set in conjunction with -source 1.5 warning: [options] source value 1.5 is obsolete and will be removed in a future release warning: [options] target value 1.5 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 16 warnings find Butterfly/src/src -name *.java -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javadoc -locale en_US -classpath /usr/share/java/commons-collections4.jar:/usr/share/java/gnu-getopt.jar:/usr/share/java/jung-algorithms.jar:/usr/share/java/jung-api.jar:/usr/share/java/jung-graph-impl.jar:/usr/share/java/jaligner.jar:debian/_jh_build.Butterfly -d debian/_jh_build.javadoc/api -quiet -notimestamp -source 1.5 Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/GraphPath.java:42: warning - @return tag has no arguments. Butterfly/src/src/My_DFS.java:563: warning - @return tag has no arguments. Butterfly/src/src/My_DFS.java:32: warning - @param argument "roots" is not a parameter name. Butterfly/src/src/PairPath.java:178: warning - @return tag has no arguments. Butterfly/src/src/PairPath.java:126: warning - @param argument "isCircular" is not a parameter name. Butterfly/src/src/Read.java:62: warning - @return tag has no arguments. Butterfly/src/src/Read.java:70: warning - @return tag has no arguments. Butterfly/src/src/Read.java:78: warning - @return tag has no arguments. Butterfly/src/src/Read.java:88: warning - @return tag has no arguments. Butterfly/src/src/Read.java:96: warning - @return tag has no arguments. Butterfly/src/src/Read.java:104: warning - @return tag has no arguments. Butterfly/src/src/Read.java:20: warning - @param argument "toV" is not a parameter name. Butterfly/src/src/SeqVertex.java:373: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:413: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:421: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:429: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:469: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:493: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:521: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:655: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:84: warning - @param argument "nextID" is not a parameter name. Butterfly/src/src/SeqVertex.java:84: warning - @param argument "l" is not a parameter name. Butterfly/src/src/SeqVertex.java:157: warning - @param argument "_origButterflyID" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "name" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "weight" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "name2" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "weight2" is not a parameter name. Butterfly/src/src/TransAssembly_allProbPaths.java:14478: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:14478: warning - @param argument "candidateNodes" is not a parameter name. Butterfly/src/src/TransAssembly_allProbPaths.java:14478: warning - @param argument "l" is not a parameter name. 42 warnings /usr/lib/jvm/default-java/bin/jar cfm /<>/trinityrnaseq-2.2.0+dfsg/Butterfly.jar ../_jh_manifest.Butterfly AlignmentStats.class BFLY_GLOBALS.class BipartiteMatching.class DFS.class GraphPath.class IsoformExpressionLearning.class ListComparator.class LocInGraph.class My_DFS$1.class My_DFS$2.class My_DFS.class NWalign.class NumPathNodeLoopsEdgeComparator.class PairPath.class PairPathWOrig.class PasaVertex$1.class PasaVertex.class Path.class PathEndSeqVertexFinishTimeComparator.class PathExpressionComparator.class PathOverlap.class PathReadSupportComparator.class PathWithOrig.class Path_n_MM_count$Vertex_path_position.class Path_n_MM_count.class Read.class ScoredPath.class SeqComparator.class SeqVertex.class SeqVertexDepthComparator.class SeqVertexFinishTimeComparator.class SeqVertexNodeDepthComparator.class SimpleEdge.class SimpleEdgeComparator.class SimplePathNodeEdge.class TopologicalSort.class TransAssembly_allProbPaths$1.class TransAssembly_allProbPaths$10.class TransAssembly_allProbPaths$11.class TransAssembly_allProbPaths$12.class TransAssembly_allProbPaths$13.class TransAssembly_allProbPaths$14.class TransAssembly_allProbPaths$15.class TransAssembly_allProbPaths$16.class TransAssembly_allProbPaths$17.class TransAssembly_allProbPaths$18.class TransAssembly_allProbPaths$19.class TransAssembly_allProbPaths$2.class TransAssembly_allProbPaths$20.class TransAssembly_allProbPaths$3.class TransAssembly_allProbPaths$4.class TransAssembly_allProbPaths$5.class TransAssembly_allProbPaths$6.class TransAssembly_allProbPaths$7.class TransAssembly_allProbPaths$8.class TransAssembly_allProbPaths$9.class TransAssembly_allProbPaths$FinalPaths.class TransAssembly_allProbPaths.class UniquePathContentComparator.class Visitor.class ZipperAlignment.class edu numLoopsEdgeComparator.class debian/rules override_dh_auto_test make[1]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg' java -cp Butterfly.jar TransAssembly_allProbPaths -N 100 -L 100 -F 300 \ -C Butterfly/src/sample_data/RawComps.0/comp0 --stderr -V 18 Started using Path alignment for path comparisons combine paths if (identity=(numberOfMatches/shorterLen) > 98.0% or if we have <= 2 mismatches) and if we have internal gap lengths <= 10 path reinforcement distance computed based on 25% of max pair distance: 300 = 75 bases SECTION ================ Parsing de Bruijn graph ====================== preProcessGraphFile: Butterfly/src/sample_data/RawComps.0/comp0.out SECTION ================== buildNewGraph ======================== buildNewGraphFirstLetter: Butterfly/src/sample_data/RawComps.0/comp0.out KMER_SIZE=24 [17] [34] [51] [68] [85] [102] [119] [136] [153] [170] [187] [204] [221] [238] [255] [272] [289] [306] [323] [340] [357] [374] [391] [408] [425] [442] [459] [476] [493] [510] [527] [544] [561] [578] [595] [612] [629] [646] [663] [680] [697] [714] [731] [748] [765] Graph is built fixExtremeleyHighSingleEdges() fixExtremelyHighSingleEdges() removeLightEdges() removeLightEdges() SECTION ================= REMOVING LIGHT In EDGES ================= SECTION ================= REMOVING LIGHT OUT EDGES ================= SECTION ================= REMOVING LIGHT FLOW EDGES ================= compactLinearPaths() SECTION ================= COMPACTING THE GRAPH ================= SNP_collapse candidates: TCAGAACAGTCATTGATATTCTTT:W5(V337_D1) len: 24 and CCAGAACAGTC:W21(V104_D1) len: 11 SECTION ==================== Removing small components. ==================== ComponentDivision: 0 contains the following vertices: node_id: 0 node_id: 128 node_id: 337 node_id: 115 node_id: 104 node_id: 361 number of good components: 1 SECTION ==================== Threading reads through the graph ========================= Threading read: SRR039231.14043245_FC42DB6AAXX:2:78:825:704, length: 75, allowing for 4 max mismatches. Read SRR039231.14043245_FC42DB6AAXX:2:78:825:704 seq TAAAGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:75,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.14043245_FC42DB6AAXX:2:78:825:704 : [0] ReadPath@Init: SRR039231.14043245_FC42DB6AAXX:2:78:825:704 : [0] Threading read: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794, length: 74, allowing for 4 max mismatches. Read SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 seq AGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:77,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] ReadPath@Init: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] Threading read: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158, length: 74, allowing for 4 max mismatches. Read SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 seq AGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:77,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0] ReadPath@Init: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0] Threading read: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027, length: 74, allowing for 4 max mismatches. Read SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 seq GGGGATCATGGTCTGAACGGAAGTTCATGANACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:78,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] ReadPath@Init: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] Threading read: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256, length: 65, allowing for 4 max mismatches. Read SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 seq AGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:68,readEnd:65] , trimmed to: [0] Threaded Read as: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0] ReadPath@Init: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0] Threading read: SRR039231.238223_FC42DB6AAXX:2:2:467:595, length: 74, allowing for 4 max mismatches. Read SRR039231.238223_FC42DB6AAXX:2:2:467:595 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:78,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] ReadPath@Init: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] Threading read: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969, length: 59, allowing for 3 max mismatches. Read SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 seq AACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:78,readEnd:59] , trimmed to: [0] Threaded Read as: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] ReadPath@Init: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] Threading read: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615, length: 75, allowing for 4 max mismatches. Read SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:79,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] ReadPath@Init: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] Threading read: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278, length: 59, allowing for 3 max mismatches. Read SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:63,readEnd:59] , trimmed to: [0] Threaded Read as: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] ReadPath@Init: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] Threading read: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587, length: 59, allowing for 3 max mismatches. Read SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:63,readEnd:59] , trimmed to: [0] Threaded Read as: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0] ReadPath@Init: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0] Threading read: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090, length: 61, allowing for 4 max mismatches. Read SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 seq GGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:66,readEnd:61] , trimmed to: [0] Threaded Read as: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0] ReadPath@Init: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0] Threading read: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133, length: 75, allowing for 4 max mismatches. Read SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 seq GGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:81,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0] ReadPath@Init: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0] Threading read: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500, length: 75, allowing for 4 max mismatches. Read SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 seq ATCATGGTCTGAACGGAAGTTCATGATAACTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:83,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 : [0] ReadPath@Init: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 : [0] Threading read: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638, length: 74, allowing for 4 max mismatches. Read SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 seq TCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:83,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0] ReadPath@Init: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0] Threading read: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567, length: 75, allowing for 4 max mismatches. Read SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 seq TCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:84,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 : [0] ReadPath@Init: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 : [0] Threading read: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026, length: 75, allowing for 4 max mismatches. Read SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 seq TCATGGTCTGAACGGAAGTTCATGATGCCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:84,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 : [0] ReadPath@Init: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 : [0] Threading read: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951, length: 70, allowing for 4 max mismatches. Read SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 seq TCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:85,readEnd:70] , trimmed to: [0] Threaded Read as: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 : [0] ReadPath@Init: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 : [0] Threading read: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016, length: 70, allowing for 4 max mismatches. Read SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 seq ATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:81,readEnd:70] , trimmed to: [0] Threaded Read as: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0] ReadPath@Init: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0] Threading read: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547, length: 74, allowing for 4 max mismatches. Read SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 seq GTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:88,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0] ReadPath@Init: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0] Threading read: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849, length: 75, allowing for 4 max mismatches. Read SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 seq GTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:89,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0] ReadPath@Init: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0] Threading read: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746, length: 75, allowing for 4 max mismatches. Read SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 seq TGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:92,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 : [0] ReadPath@Init: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 : [0] Threading read: SRR039231.14173065_FC42DB6AAXX:2:79:322:765, length: 75, allowing for 4 max mismatches. Read SRR039231.14173065_FC42DB6AAXX:2:79:322:765 seq TGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:92,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.14173065_FC42DB6AAXX:2:79:322:765 : [0] ReadPath@Init: SRR039231.14173065_FC42DB6AAXX:2:79:322:765 : [0] Threading read: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344, length: 69, allowing for 4 max mismatches. Read SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 seq GAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:92,readEnd:69] , trimmed to: [0] Threaded Read as: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 : [0] ReadPath@Init: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 : [0] Threading read: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828, length: 75, allowing for 4 max mismatches. Read SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 seq GAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:93,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 : [0] ReadPath@Init: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 : [0] Threading read: SRR039231.238223_FC42DB6AAXX:2:2:467:595, length: 75, allowing for 4 max mismatches. Read SRR039231.238223_FC42DB6AAXX:2:2:467:595 seq GATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:107,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] ReadPath@Init: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] Threading read: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442, length: 75, allowing for 4 max mismatches. Read SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 seq TACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:109,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 : [0] ReadPath@Init: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 : [0] Threading read: SRR039231.21589259_FC42DB6AAXX:2:119:947:546, length: 75, allowing for 4 max mismatches. Read SRR039231.21589259_FC42DB6AAXX:2:119:947:546 seq ACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:110,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.21589259_FC42DB6AAXX:2:119:947:546 : [0] ReadPath@Init: SRR039231.21589259_FC42DB6AAXX:2:119:947:546 : [0] Threading read: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833, length: 75, allowing for 4 max mismatches. Read SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 seq CTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:112,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0] ReadPath@Init: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0] Threading read: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177, length: 75, allowing for 4 max mismatches. Read SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 seq CTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:112,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0] ReadPath@Init: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0] Threading read: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867, length: 68, allowing for 4 max mismatches. Read SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 seq TAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:106,readEnd:68] , trimmed to: [0] Threaded Read as: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [0] ReadPath@Init: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [0] Threading read: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027, length: 75, allowing for 4 max mismatches. Read SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 seq AGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCNTCTGGTACATTTCATGGCTGAGAAAACATTTTTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:114,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] ReadPath@Init: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] Threading read: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536, length: 64, allowing for 4 max mismatches. Read SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 seq ATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:106,readEnd:64] , trimmed to: [0] Threaded Read as: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0] ReadPath@Init: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0] Threading read: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794, length: 75, allowing for 4 max mismatches. Read SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] ReadPath@Init: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] Threading read: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615, length: 75, allowing for 4 max mismatches. Read SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] ReadPath@Init: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] Threading read: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278, length: 75, allowing for 4 max mismatches. Read SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] ReadPath@Init: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] Threading read: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969, length: 75, allowing for 4 max mismatches. Read SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] ReadPath@Init: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] Threading read: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090, length: 75, allowing for 4 max mismatches. Read SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 seq GATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:74] [337,nodeEnd:24,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0, 337] ReadPath@Init: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0, 337] Threading read: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849, length: 75, allowing for 4 max mismatches. Read SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 seq GATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:74] [104,nodeEnd:24,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0, 104] ReadPath@Init: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0, 104] Threading read: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158, length: 75, allowing for 4 max mismatches. Read SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 seq ATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:73] [104,nodeEnd:25,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0, 104] ReadPath@Init: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0, 104] Threading read: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016, length: 74, allowing for 4 max mismatches. Read SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 seq ATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:73] [104,nodeEnd:24,readEnd:74] , trimmed to: [0, 104] Threaded Read as: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0, 104] ReadPath@Init: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0, 104] Threading read: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547, length: 75, allowing for 4 max mismatches. Read SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 seq ATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:71] [104,nodeEnd:27,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0, 104] ReadPath@Init: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0, 104] Threading read: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638, length: 75, allowing for 4 max mismatches. Read SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 seq GATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:69] [337,nodeEnd:29,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0, 337] ReadPath@Init: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0, 337] Threading read: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587, length: 75, allowing for 4 max mismatches. Read SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 seq GATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:69] [104,nodeEnd:29,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0, 104] ReadPath@Init: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0, 104] Threading read: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288, length: 75, allowing for 4 max mismatches. Read SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 seq TGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:67] [104,nodeEnd:31,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104] ReadPath@Init: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104] Threading read: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333, length: 72, allowing for 4 max mismatches. Read SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:66] [104,nodeEnd:29,readEnd:72] , trimmed to: [0, 104] Threaded Read as: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [0, 104] ReadPath@Init: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [0, 104] Threading read: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450, length: 53, allowing for 3 max mismatches. Read SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 seq GGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:44] [337,nodeEnd:32,readEnd:53] , trimmed to: [0, 337] Threaded Read as: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [0, 337] ReadPath@Init: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [0, 337] Threading read: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595, length: 72, allowing for 4 max mismatches. Read SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:66] [337,nodeEnd:29,readEnd:72] , trimmed to: [0, 337] Threaded Read as: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [0, 337] ReadPath@Init: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [0, 337] Threading read: SRR039231.2140780_FC42DB6AAXX:2:12:746:731, length: 56, allowing for 3 max mismatches. Read SRR039231.2140780_FC42DB6AAXX:2:12:746:731 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:117,readEnd:56] , trimmed to: [0] Threaded Read as: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0] ReadPath@Init: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0] Threading read: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289, length: 69, allowing for 4 max mismatches. Read SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:66] [104,nodeEnd:26,readEnd:69] , trimmed to: [0, 104] Threaded Read as: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [0, 104] ReadPath@Init: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [0, 104] Threading read: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566, length: 57, allowing for 3 max mismatches. Read SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:118,readEnd:57] , trimmed to: [0] Threaded Read as: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [0] ReadPath@Init: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [0] Threading read: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161, length: 70, allowing for 4 max mismatches. Read SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 seq TCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAGT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:60] [337,nodeEnd:33,readEnd:70] , trimmed to: [0, 337] Threaded Read as: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [0, 337] ReadPath@Init: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [0, 337] Threading read: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256, length: 75, allowing for 4 max mismatches. Read SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 seq TGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:64] [104,nodeEnd:34,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0, 104] ReadPath@Init: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0, 104] Threading read: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133, length: 75, allowing for 4 max mismatches. Read SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 seq TGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:64] [337,nodeEnd:34,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0, 337] ReadPath@Init: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0, 337] Threading read: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457, length: 75, allowing for 4 max mismatches. Read SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 seq GATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:62] [337,nodeEnd:36,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [0, 337] ReadPath@Init: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [0, 337] Threading read: SRR039231.21001541_FC42DB6AAXX:2:116:708:497, length: 75, allowing for 4 max mismatches. Read SRR039231.21001541_FC42DB6AAXX:2:116:708:497 seq ATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:61] [104,nodeEnd:34,readEnd:72] [115,nodeEnd:26,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115] ReadPath@Init: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115] Threading read: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375, length: 75, allowing for 4 max mismatches. Read SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 seq ATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:61] [104,nodeEnd:34,readEnd:72] [115,nodeEnd:26,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [0, 104, 115] ReadPath@Init: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [0, 104, 115] Threading read: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254, length: 74, allowing for 4 max mismatches. Read SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 seq TCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:60] [104,nodeEnd:34,readEnd:71] [115,nodeEnd:26,readEnd:74] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [0, 104, 115] ReadPath@Init: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [0, 104, 115] Threading read: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346, length: 75, allowing for 4 max mismatches. Read SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 seq TAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:58] [104,nodeEnd:34,readEnd:69] [115,nodeEnd:29,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [0, 104, 115] ReadPath@Init: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [0, 104, 115] Threading read: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604, length: 67, allowing for 4 max mismatches. Read SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 seq TAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:58] [104,nodeEnd:32,readEnd:67] , trimmed to: [0, 104] Threaded Read as: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [0, 104] ReadPath@Init: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [0, 104] Threading read: SRR039231.14735089_FC42DB6AAXX:2:82:509:413, length: 75, allowing for 4 max mismatches. WARNING, Tied paths from vertex [V0 ]: Path A: PATH_N_MM_COUNT: mismatches=0, path= [104, 115] positions: [104,nodeEnd:34,readEnd:67] [115,nodeEnd:31,readEnd:75] vs. Path B: PATH_N_MM_COUNT: mismatches=1, path= [337] positions: [337,nodeEnd:42,readEnd:75] WARNING: TIED_READ_PATH Read SRR039231.14735089_FC42DB6AAXX:2:82:509:413 seq GAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTTATGGTTTGATGAACCAGAACAGTCATTGATAT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:56] [104,nodeEnd:34,readEnd:67] [115,nodeEnd:31,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [0, 104, 115] ReadPath@Init: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [0, 104, 115] Threading read: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833, length: 75, allowing for 4 max mismatches. Read SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 seq AGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:52] [104,nodeEnd:34,readEnd:63] [115,nodeEnd:35,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0, 104, 115] ReadPath@Init: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0, 104, 115] Threading read: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177, length: 75, allowing for 4 max mismatches. WARNING, Tied paths from vertex [V0 ]: Path A: PATH_N_MM_COUNT: mismatches=0, path= [104, 115] positions: [104,nodeEnd:34,readEnd:62] [115,nodeEnd:36,readEnd:75] vs. Path B: PATH_N_MM_COUNT: mismatches=1, path= [337] positions: [337,nodeEnd:47,readEnd:75] WARNING: TIED_READ_PATH Read SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 seq GGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGGTGGTTTGATGAACCAGAACAGTCATTGATATTCTTT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:51] [104,nodeEnd:34,readEnd:62] [115,nodeEnd:36,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0, 104, 115] ReadPath@Init: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0, 104, 115] Threading read: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560, length: 75, allowing for 4 max mismatches. Read SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 seq GGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:51] [104,nodeEnd:34,readEnd:62] [115,nodeEnd:36,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [0, 104, 115] ReadPath@Init: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [0, 104, 115] Threading read: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562, length: 51, allowing for 3 max mismatches. Read SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 seq CTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:46] [104,nodeEnd:28,readEnd:51] , trimmed to: [0, 104] Threaded Read as: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 : [0, 104] ReadPath@Init: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 : [0, 104] Threading read: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691, length: 75, allowing for 4 max mismatches. Read SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 seq CTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:46] [104,nodeEnd:34,readEnd:57] [115,nodeEnd:36,readEnd:70] [128,nodeEnd:28,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 : [0, 104, 115, 128] ReadPath@Init: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 : [0, 104, 115, 128] Threading read: SRR039231.2140780_FC42DB6AAXX:2:12:746:731, length: 75, allowing for 4 max mismatches. Read SRR039231.2140780_FC42DB6AAXX:2:12:746:731 seq ATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:39] [104,nodeEnd:34,readEnd:50] [115,nodeEnd:36,readEnd:63] [128,nodeEnd:35,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0, 104, 115, 128] ReadPath@Init: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0, 104, 115, 128] Threading read: SRR039231.21001541_FC42DB6AAXX:2:116:708:497, length: 75, allowing for 4 max mismatches. Read SRR039231.21001541_FC42DB6AAXX:2:116:708:497 seq TCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:36] [104,nodeEnd:34,readEnd:47] [115,nodeEnd:36,readEnd:60] [128,nodeEnd:38,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115, 128] ReadPath@Init: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115, 128] Threading read: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110, length: 70, allowing for 4 max mismatches. Read SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 seq GAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:26] [104,nodeEnd:34,readEnd:37] [115,nodeEnd:36,readEnd:50] [128,nodeEnd:43,readEnd:70] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [0, 104, 115, 128] ReadPath@Init: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [0, 104, 115, 128] Threading read: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536, length: 75, allowing for 4 max mismatches. -running Needleman-Wunsch alignment of vertex to read Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh construct INFO: Started... Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh construct INFO: Finished. Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh traceback INFO: Started... Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. Vertex 1 TCAGAACAGTCATTGATATTCTTT 24 .||||||||||||:|||||||||| Read 1 CCAGAACAGTCATNGATATTCTTT 24 Read SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 seq GCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATNGATATTCTTTATAAGCATATTCAAGCGCAC threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:31] [104,nodeEnd:34,readEnd:42] [115,nodeEnd:36,readEnd:55] [128,nodeEnd:43,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0, 104, 115, 128] ReadPath@Init: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0, 104, 115, 128] Threading read: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35, length: 75, allowing for 4 max mismatches. Read SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 seq GAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:28] [104,nodeEnd:34,readEnd:39] [115,nodeEnd:36,readEnd:52] [128,nodeEnd:46,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [0, 104, 115, 128] ReadPath@Init: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [0, 104, 115, 128] Threading read: SRR039231.142909_FC42DB6AAXX:2:1:1346:135, length: 75, allowing for 4 max mismatches. Read SRR039231.142909_FC42DB6AAXX:2:1:1346:135 seq AGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:27] [104,nodeEnd:34,readEnd:38] [115,nodeEnd:36,readEnd:51] [128,nodeEnd:47,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [0, 104, 115, 128] ReadPath@Init: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [0, 104, 115, 128] Threading read: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560, length: 75, allowing for 4 max mismatches. Read SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 seq GAAAACATTTTTGGTGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [361, 115, 128] positions: [361,nodeEnd:47,readEnd:37] [115,nodeEnd:36,readEnd:50] [128,nodeEnd:48,readEnd:75] , trimmed to: [361, 115, 128] Threaded Read as: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [361, 115, 128] ReadPath@Init: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [361, 115, 128] Threading read: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968, length: 75, allowing for 4 max mismatches. -running Needleman-Wunsch alignment of vertex to read Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh construct INFO: Started... Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh construct INFO: Finished. Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh traceback INFO: Started... Aug 29, 2016 3:52:05 PM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. Vertex 1 TCAGAACAGTCATTGATATTCTTT 24 .|||||||||||||:||||||||| Read 1 CCAGAACAGTCATTNATATTCTTT 24 Read SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 seq AAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTNATATTCTTTATAAGCATATTCAAGCGCACTGGAAAT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:24] [104,nodeEnd:34,readEnd:35] [115,nodeEnd:36,readEnd:48] [128,nodeEnd:50,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [0, 104, 115, 128] ReadPath@Init: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [0, 104, 115, 128] Threading read: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288, length: 75, allowing for 4 max mismatches. Read SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 seq AAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:24] [104,nodeEnd:34,readEnd:35] [115,nodeEnd:36,readEnd:48] [128,nodeEnd:50,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104, 115, 128] ReadPath@Init: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104, 115, 128] Threading read: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867, length: 75, allowing for 4 max mismatches. Read SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 seq AACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [104, 115, 128] positions: [104,nodeEnd:34,readEnd:34] [115,nodeEnd:36,readEnd:47] [128,nodeEnd:51,readEnd:75] , trimmed to: [104, 115, 128] Threaded Read as: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [104, 115, 128] ReadPath@Init: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [104, 115, 128] Threading read: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457, length: 75, allowing for 4 max mismatches. Read SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 seq TTTTGATGGTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:42] [128,nodeEnd:56,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [337, 128] ReadPath@Init: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [337, 128] Threading read: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450, length: 67, allowing for 4 max mismatches. Read SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 seq TTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:33] [128,nodeEnd:57,readEnd:67] , trimmed to: [337, 128] Threaded Read as: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [337, 128] ReadPath@Init: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [337, 128] Threading read: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595, length: 75, allowing for 4 max mismatches. Read SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 seq TTTGATGGTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:41] [128,nodeEnd:57,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [337, 128] ReadPath@Init: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [337, 128] Threading read: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566, length: 58, allowing for 3 max mismatches. Read SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:57,readEnd:58] , trimmed to: [115, 128] Threaded Read as: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [115, 128] ReadPath@Init: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [115, 128] Threading read: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333, length: 60, allowing for 3 max mismatches. Read SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:59,readEnd:60] , trimmed to: [115, 128] Threaded Read as: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [115, 128] ReadPath@Init: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [115, 128] Threading read: SRR039231.390226_FC42DB6AAXX:2:3:125:1502, length: 75, allowing for 4 max mismatches. Read SRR039231.390226_FC42DB6AAXX:2:3:125:1502 seq GGTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:35] [128,nodeEnd:63,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] ReadPath@Init: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] Threading read: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312, length: 75, allowing for 4 max mismatches. Read SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 seq GTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [337, 128] ReadPath@Init: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [337, 128] Threading read: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958, length: 75, allowing for 4 max mismatches. Read SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 seq GTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [115, 128] ReadPath@Init: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [115, 128] Threading read: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254, length: 75, allowing for 4 max mismatches. Read SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 seq GTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [115, 128] ReadPath@Init: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [115, 128] Threading read: SRR039231.8633607_FC42DB6AAXX:2:48:203:527, length: 75, allowing for 4 max mismatches. Read SRR039231.8633607_FC42DB6AAXX:2:48:203:527 seq GTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [115, 128] ReadPath@Init: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [115, 128] Threading read: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161, length: 75, allowing for 4 max mismatches. Read SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 seq ATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:29] [128,nodeEnd:69,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [337, 128] ReadPath@Init: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [337, 128] Threading read: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289, length: 66, allowing for 4 max mismatches. Read SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 seq ATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:29] [128,nodeEnd:60,readEnd:66] , trimmed to: [115, 128] Threaded Read as: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [115, 128] ReadPath@Init: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [115, 128] Threading read: SRR039231.14735089_FC42DB6AAXX:2:82:509:413, length: 75, allowing for 4 max mismatches. Read SRR039231.14735089_FC42DB6AAXX:2:82:509:413 seq TGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:28] [128,nodeEnd:70,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [115, 128] ReadPath@Init: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [115, 128] Threading read: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769, length: 65, allowing for 4 max mismatches. Read SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 seq CAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:70,readEnd:65] , trimmed to: [128] Threaded Read as: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 : [128] ReadPath@Init: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 : [128] Threading read: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35, length: 69, allowing for 4 max mismatches. Read SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 seq AGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:70,readEnd:69] , trimmed to: [128] Threaded Read as: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [128] ReadPath@Init: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [128] Threading read: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375, length: 75, allowing for 4 max mismatches. Read SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 seq TGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:28] [128,nodeEnd:70,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [115, 128] ReadPath@Init: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [115, 128] Threading read: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604, length: 72, allowing for 4 max mismatches. Read SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:71,readEnd:72] , trimmed to: [115, 128] Threaded Read as: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [115, 128] ReadPath@Init: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [115, 128] Threading read: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887, length: 70, allowing for 4 max mismatches. Read SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 seq AGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:71,readEnd:70] , trimmed to: [128] Threaded Read as: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 : [128] ReadPath@Init: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 : [128] Threading read: SRR039231.390226_FC42DB6AAXX:2:3:125:1502, length: 75, allowing for 4 max mismatches. Read SRR039231.390226_FC42DB6AAXX:2:3:125:1502 seq GAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAATCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [337, 128] positions: [337,nodeEnd:47,readEnd:27] [128,nodeEnd:71,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] ReadPath@Init: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] Threading read: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968, length: 72, allowing for 4 max mismatches. Read SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:71,readEnd:72] , trimmed to: [115, 128] Threaded Read as: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [115, 128] ReadPath@Init: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [115, 128] Threading read: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346, length: 75, allowing for 4 max mismatches. Read SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 seq AGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:76,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [128] ReadPath@Init: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [128] Threading read: SRR039231.142909_FC42DB6AAXX:2:1:1346:135, length: 75, allowing for 4 max mismatches. Read SRR039231.142909_FC42DB6AAXX:2:1:1346:135 seq GTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:82,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [128] ReadPath@Init: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [128] Threading read: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958, length: 75, allowing for 4 max mismatches. Read SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 seq TATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:90,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [128] ReadPath@Init: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [128] Threading read: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312, length: 57, allowing for 3 max mismatches. Read SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 seq CAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:91,readEnd:57] , trimmed to: [128] Threaded Read as: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [128] ReadPath@Init: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [128] Threading read: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110, length: 75, allowing for 4 max mismatches. Read SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 seq TTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:95,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [128] ReadPath@Init: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [128] Threading read: SRR039231.8633607_FC42DB6AAXX:2:48:203:527, length: 75, allowing for 4 max mismatches. Read SRR039231.8633607_FC42DB6AAXX:2:48:203:527 seq TATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:97,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [128] ReadPath@Init: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [128] Threading read: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158, length: 64, allowing for 4 max mismatches. Read SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 seq AATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:111,readEnd:64] , trimmed to: [128] Threaded Read as: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 : [128] ReadPath@Init: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 : [128] Threading read: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404, length: 75, allowing for 4 max mismatches. Read SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 seq GCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:112,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 : [128] ReadPath@Init: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 : [128] Threading read: SRR039231.16895577_FC42DB6AAXX:2:94:163:51, length: 75, allowing for 4 max mismatches. Read SRR039231.16895577_FC42DB6AAXX:2:94:163:51 seq GCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:112,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.16895577_FC42DB6AAXX:2:94:163:51 : [128] ReadPath@Init: SRR039231.16895577_FC42DB6AAXX:2:94:163:51 : [128] Threading read: SRR039231.3014932_FC42DB6AAXX:2:17:237:179, length: 75, allowing for 4 max mismatches. Read SRR039231.3014932_FC42DB6AAXX:2:17:237:179 seq GCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:112,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] ReadPath@Init: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] Threading read: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782, length: 75, allowing for 4 max mismatches. Read SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 seq CGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:113,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] ReadPath@Init: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] Threading read: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065, length: 75, allowing for 4 max mismatches. Read SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 seq GGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:133,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] ReadPath@Init: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] Threading read: SRR039231.21734868_FC42DB6AAXX:2:120:549:795, length: 75, allowing for 4 max mismatches. Read SRR039231.21734868_FC42DB6AAXX:2:120:549:795 seq GTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:134,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] ReadPath@Init: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] Threading read: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782, length: 75, allowing for 4 max mismatches. Read SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 seq GTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:134,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] ReadPath@Init: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] Threading read: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880, length: 74, allowing for 4 max mismatches. Read SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:152,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] ReadPath@Init: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] Threading read: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996, length: 74, allowing for 4 max mismatches. Read SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:152,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] ReadPath@Init: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] Threading read: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670, length: 75, allowing for 4 max mismatches. Read SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 : [128] ReadPath@Init: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 : [128] Threading read: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397, length: 70, allowing for 4 max mismatches. Read SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 seq GTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:70] , trimmed to: [128] Threaded Read as: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] ReadPath@Init: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] Threading read: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147, length: 75, allowing for 4 max mismatches. Read SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] ReadPath@Init: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] Threading read: SRR039231.624520_FC42DB6AAXX:2:4:581:550, length: 75, allowing for 4 max mismatches. Read SRR039231.624520_FC42DB6AAXX:2:4:581:550 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] ReadPath@Init: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] Threading read: SRR039231.939493_FC42DB6AAXX:2:5:1771:471, length: 75, allowing for 4 max mismatches. Read SRR039231.939493_FC42DB6AAXX:2:5:1771:471 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] ReadPath@Init: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] Threading read: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734, length: 65, allowing for 4 max mismatches. Read SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 seq GACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:154,readEnd:65] , trimmed to: [128] Threaded Read as: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] ReadPath@Init: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] Threading read: SRR039231.16173078_FC42DB6AAXX:2:90:254:422, length: 75, allowing for 4 max mismatches. Read SRR039231.16173078_FC42DB6AAXX:2:90:254:422 seq CCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:154,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] ReadPath@Init: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] Threading read: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895, length: 75, allowing for 4 max mismatches. Read SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 : [128] ReadPath@Init: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 : [128] Threading read: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229, length: 67, allowing for 4 max mismatches. Read SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 seq CGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:67] , trimmed to: [128] Threaded Read as: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] ReadPath@Init: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] Threading read: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281, length: 75, allowing for 4 max mismatches. Read SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] ReadPath@Init: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] Threading read: SRR039231.17068078_FC42DB6AAXX:2:95:58:257, length: 75, allowing for 4 max mismatches. Read SRR039231.17068078_FC42DB6AAXX:2:95:58:257 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] ReadPath@Init: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] Threading read: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670, length: 75, allowing for 4 max mismatches. Read SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] ReadPath@Init: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] Threading read: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073, length: 75, allowing for 4 max mismatches. Read SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 : [128] ReadPath@Init: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 : [128] Threading read: SRR039231.9196619_FC42DB6AAXX:2:51:473:936, length: 75, allowing for 4 max mismatches. Read SRR039231.9196619_FC42DB6AAXX:2:51:473:936 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] ReadPath@Init: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] Threading read: SRR039231.1328085_FC42DB6AAXX:2:8:132:68, length: 75, allowing for 4 max mismatches. Read SRR039231.1328085_FC42DB6AAXX:2:8:132:68 seq CAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:156,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] ReadPath@Init: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] Threading read: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591, length: 75, allowing for 4 max mismatches. Read SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 seq CAGTTTTCGACATCTCCTATTTCTTNGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGC threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:156,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] ReadPath@Init: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] Threading read: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689, length: 75, allowing for 4 max mismatches. Read SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 seq CAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:156,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] ReadPath@Init: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] Threading read: SRR039231.3014932_FC42DB6AAXX:2:17:237:179, length: 75, allowing for 4 max mismatches. Read SRR039231.3014932_FC42DB6AAXX:2:17:237:179 seq TCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:162,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] ReadPath@Init: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] Threading read: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859, length: 75, allowing for 4 max mismatches. Read SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 seq CTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:169,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] ReadPath@Init: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] Threading read: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065, length: 39, allowing for 2 max mismatches. Read SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 seq AAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:170,readEnd:39] , trimmed to: [128] Threaded Read as: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] ReadPath@Init: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] Threading read: SRR039231.5836358_FC42DB6AAXX:2:32:993:352, length: 75, allowing for 4 max mismatches. Read SRR039231.5836358_FC42DB6AAXX:2:32:993:352 seq CTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:172,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] ReadPath@Init: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] Threading read: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689, length: 75, allowing for 4 max mismatches. Read SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 seq TGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:181,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] ReadPath@Init: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] Threading read: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723, length: 72, allowing for 4 max mismatches. Read SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 seq GCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:183,readEnd:72] , trimmed to: [128] Threaded Read as: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] ReadPath@Init: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] Threading read: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021, length: 71, allowing for 4 max mismatches. Read SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 seq CATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGGTTAGCAAAAGTAAGGGCACTTTGATGGAGT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:186,readEnd:71] , trimmed to: [128] Threaded Read as: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 : [128] ReadPath@Init: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 : [128] Threading read: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391, length: 75, allowing for 4 max mismatches. Read SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 seq CTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:187,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 : [128] ReadPath@Init: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 : [128] Threading read: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880, length: 66, allowing for 4 max mismatches. Read SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 seq TTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:189,readEnd:66] , trimmed to: [128] Threaded Read as: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] ReadPath@Init: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] Threading read: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481, length: 75, allowing for 4 max mismatches. Read SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 seq CATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:190,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 : [128] ReadPath@Init: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 : [128] Threading read: SRR039231.939493_FC42DB6AAXX:2:5:1771:471, length: 75, allowing for 4 max mismatches. Read SRR039231.939493_FC42DB6AAXX:2:5:1771:471 seq CATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:190,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] ReadPath@Init: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] Threading read: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099, length: 75, allowing for 4 max mismatches. Read SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 seq ATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:191,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] ReadPath@Init: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] Threading read: SRR039231.1328085_FC42DB6AAXX:2:8:132:68, length: 46, allowing for 3 max mismatches. Read SRR039231.1328085_FC42DB6AAXX:2:8:132:68 seq CAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:173,readEnd:46] , trimmed to: [128] Threaded Read as: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] ReadPath@Init: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] Threading read: SRR039231.17068078_FC42DB6AAXX:2:95:58:257, length: 75, allowing for 4 max mismatches. Read SRR039231.17068078_FC42DB6AAXX:2:95:58:257 seq AAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:194,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] ReadPath@Init: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] Threading read: SRR039231.21734868_FC42DB6AAXX:2:120:549:795, length: 75, allowing for 4 max mismatches. Read SRR039231.21734868_FC42DB6AAXX:2:120:549:795 seq AAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:194,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] ReadPath@Init: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] Threading read: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734, length: 75, allowing for 4 max mismatches. Read SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 seq AAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:195,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] ReadPath@Init: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] Threading read: SRR039231.16173078_FC42DB6AAXX:2:90:254:422, length: 75, allowing for 4 max mismatches. Read SRR039231.16173078_FC42DB6AAXX:2:90:254:422 seq AAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:195,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] ReadPath@Init: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] Threading read: SRR039231.624520_FC42DB6AAXX:2:4:581:550, length: 68, allowing for 4 max mismatches. Read SRR039231.624520_FC42DB6AAXX:2:4:581:550 seq CAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:195,readEnd:68] , trimmed to: [128] Threaded Read as: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] ReadPath@Init: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] Threading read: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397, length: 66, allowing for 4 max mismatches. Read SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 seq GGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:199,readEnd:66] , trimmed to: [128] Threaded Read as: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] ReadPath@Init: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] Threading read: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147, length: 74, allowing for 4 max mismatches. Read SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 seq CAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:201,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] ReadPath@Init: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] Threading read: SRR039231.9196619_FC42DB6AAXX:2:51:473:936, length: 68, allowing for 4 max mismatches. Read SRR039231.9196619_FC42DB6AAXX:2:51:473:936 seq GGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:201,readEnd:68] , trimmed to: [128] Threaded Read as: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] ReadPath@Init: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] Threading read: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281, length: 75, allowing for 4 max mismatches. Read SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 seq AACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:203,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] ReadPath@Init: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] Threading read: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996, length: 71, allowing for 4 max mismatches. Read SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 seq GGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:204,readEnd:71] , trimmed to: [128] Threaded Read as: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] ReadPath@Init: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] Threading read: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592, length: 65, allowing for 4 max mismatches. Read SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 seq CATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:206,readEnd:65] , trimmed to: [128] Threaded Read as: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 : [128] ReadPath@Init: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 : [128] Threading read: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670, length: 75, allowing for 4 max mismatches. Read SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 seq AGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:211,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] ReadPath@Init: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] Threading read: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229, length: 75, allowing for 4 max mismatches. Read SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 seq AGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:213,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] ReadPath@Init: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] Threading read: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859, length: 75, allowing for 4 max mismatches. Read SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 seq CCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:215,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] ReadPath@Init: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] Threading read: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591, length: 74, allowing for 4 max mismatches. Read SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 seq CCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:214,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] ReadPath@Init: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] Threading read: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499, length: 75, allowing for 4 max mismatches. Read SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 seq ATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:217,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 : [128] ReadPath@Init: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 : [128] Threading read: SRR039231.5836358_FC42DB6AAXX:2:32:993:352, length: 75, allowing for 4 max mismatches. Read SRR039231.5836358_FC42DB6AAXX:2:32:993:352 seq ATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:217,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] ReadPath@Init: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] Threading read: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473, length: 70, allowing for 4 max mismatches. Read SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 seq GTTGAGTCTGCTTAGCAAAAGTAAGAGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:215,readEnd:70] , trimmed to: [128] Threaded Read as: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 : [128] ReadPath@Init: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 : [128] Threading read: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099, length: 75, allowing for 4 max mismatches. Read SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 seq CTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:227,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] ReadPath@Init: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] Threading read: SRR039231.1908187_FC42DB6AAXX:2:11:306:275, length: 75, allowing for 4 max mismatches. Read SRR039231.1908187_FC42DB6AAXX:2:11:306:275 seq GCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGCTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:229,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.1908187_FC42DB6AAXX:2:11:306:275 : [128] ReadPath@Init: SRR039231.1908187_FC42DB6AAXX:2:11:306:275 : [128] Threading read: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711, length: 72, allowing for 4 max mismatches. Read SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 seq AGCAAAAGTAAGGGCACTTTGATGGATTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGCTTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:230,readEnd:72] , trimmed to: [128] Threaded Read as: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 : [128] ReadPath@Init: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 : [128] Threading read: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723, length: 75, allowing for 4 max mismatches. Read SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 seq TAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGCTTGTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:232,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] ReadPath@Init: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] number of reads found = 163 (from total of 163) which came from 96 pairs Read name to pairing info: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 => [0][0, 104, 115, 128] Read name to pairing info: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 => [0, 337][337, 128] Read name to pairing info: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 => [128][128] Read name to pairing info: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 => [128][128] Read name to pairing info: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 => [0][0] Read name to pairing info: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 => [0][0] Read name to pairing info: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 => [0] Read name to pairing info: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 => [0][115, 128] Read name to pairing info: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 => [128] Read name to pairing info: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 => [0, 104, 115][0, 104, 115, 128] Read name to pairing info: SRR039231.21589259_FC42DB6AAXX:2:119:947:546 => [0] Read name to pairing info: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 => [0, 104, 115][361, 115, 128] Read name to pairing info: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 => [0, 104, 115][115, 128] Read name to pairing info: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 => [115, 128][128] Read name to pairing info: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 => [128][128] Read name to pairing info: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 => [128][128] Read name to pairing info: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 => [128][128] Read name to pairing info: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 => [0] Read name to pairing info: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 => [128] Read name to pairing info: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 => [0][0, 104] Read name to pairing info: SRR039231.14173065_FC42DB6AAXX:2:79:322:765 => [0] Read name to pairing info: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 => [0][0, 104] Read name to pairing info: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 => [128] Read name to pairing info: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 => [0][0, 104] Read name to pairing info: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 => [128] Read name to pairing info: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 => [128][128] Read name to pairing info: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 => [128] Read name to pairing info: SRR039231.624520_FC42DB6AAXX:2:4:581:550 => [128][128] Read name to pairing info: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 => [128] Read name to pairing info: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 => [0, 104, 115, 128][115, 128] Read name to pairing info: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 => [0] Read name to pairing info: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 => [0] Read name to pairing info: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 => [0, 104][0, 104, 115, 128] Read name to pairing info: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 => [0][0, 104, 115] Read name to pairing info: SRR039231.1908187_FC42DB6AAXX:2:11:306:275 => [128] Read name to pairing info: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 => [128][128] Read name to pairing info: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 => [128] Read name to pairing info: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 => [0][104, 115, 128] Read name to pairing info: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 => [0][0, 337] Read name to pairing info: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 => [128][128] Read name to pairing info: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 => [0][0, 337] Read name to pairing info: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 => [0] Read name to pairing info: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 => [0][0, 104] Read name to pairing info: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 => [128] Read name to pairing info: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 => [0][0, 104] Read name to pairing info: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 => [0, 104, 115][115, 128] Read name to pairing info: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 => [0] Read name to pairing info: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 => [128][128] Read name to pairing info: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 => [0] Read name to pairing info: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 => [0, 104][115, 128] Read name to pairing info: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 => [337, 128][337, 128] Read name to pairing info: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 => [0, 104, 115][128] Read name to pairing info: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 => [0, 104, 115, 128][128] Read name to pairing info: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 => [128] Read name to pairing info: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 => [0][0, 337] Read name to pairing info: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 => [128][128] Read name to pairing info: SRR039231.16895577_FC42DB6AAXX:2:94:163:51 => [128] Read name to pairing info: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 => [128] Read name to pairing info: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 => [0, 337][337, 128] Read name to pairing info: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 => [337, 128][128] Read name to pairing info: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 => [128] Read name to pairing info: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 => [0, 104][115, 128] Read name to pairing info: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 => [115, 128][128] Read name to pairing info: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 => [128] Read name to pairing info: SRR039231.14043245_FC42DB6AAXX:2:78:825:704 => [0] Read name to pairing info: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 => [0, 104] Read name to pairing info: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 => [128] Read name to pairing info: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 => [0, 104, 115, 128] Read name to pairing info: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 => [128][128] Read name to pairing info: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 => [128][128] Read name to pairing info: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 => [0][0, 104, 115, 128] Read name to pairing info: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 => [128][128] Read name to pairing info: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 => [0, 337][337, 128] Read name to pairing info: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 => [0, 337][337, 128] Read name to pairing info: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 => [128][128] Read name to pairing info: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 => [128] Read name to pairing info: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 => [0, 104, 115, 128][128] Read name to pairing info: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 => [128][128] Read name to pairing info: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 => [128][128] Read name to pairing info: SRR039231.238223_FC42DB6AAXX:2:2:467:595 => [0][0] Read name to pairing info: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 => [0][0] Read name to pairing info: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 => [0, 104, 115][115, 128] Read name to pairing info: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 => [128][128] Read name to pairing info: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 => [0][0] Read name to pairing info: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 => [128][128] Read name to pairing info: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 => [128][128] Read name to pairing info: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 => [0, 104][115, 128] Read name to pairing info: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 => [0][0] Read name to pairing info: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 => [0, 104, 115, 128][128] Read name to pairing info: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 => [0][0, 104] Read name to pairing info: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 => [128][128] Read name to pairing info: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 => [0][0, 104, 115] Read name to pairing info: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 => [128][128] Read name to pairing info: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 => [0] Read name to pairing info: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 => [128][128] Read name to pairing info: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 => [128][128] SECTION ================== Pairing up the reads into PairPaths =========================== we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [0, 104, 115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [361, 115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[115, 128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 4 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 5 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 3 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 6 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 7 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104], [0, 104, 115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115]]] we have 8 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [104, 115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 337]]] we have 9 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 337]]] we have 4 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 5 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 104, 115], [115, 128]]] we have 10 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[337, 128], [337, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[0], [0, 337]]] we have 11 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[337, 128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 104], [115, 128]]] we have 2 reads supporting the path: PairPath [_paths=[[115, 128], [128]]] we have 12 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 13 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115, 128]]] we have 14 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 4 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 15 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [128]]] we have 16 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 17 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 4 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 104, 115], [115, 128]]] we have 18 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 5 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 19 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 20 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 104], [115, 128]]] we have 6 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [128]]] we have 6 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 21 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115]]] we have 22 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 23 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 24 reads supporting the path: PairPath [_paths=[[128], [128]]] number of reads used = 96 ## Read PathPair results: 29 singletons, num pairs: 67, num pairs discarded: 0 Printing Pair Paths Before DAG Overlap Layout ------------------ Start Vertex:0 PairPaths@Init: PairPath [_paths=[[0], [0]]]=6 PairPaths@Init: PairPath [_paths=[[0], []]]=11 PairPaths@Init: PairPath [_paths=[[0, 104], [115, 128]]]=3 PairPaths@Init: PairPath [_paths=[[0], [0, 104]]]=6 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [115, 128]]]=3 PairPaths@Init: PairPath [_paths=[[0], [0, 104, 115]]]=2 PairPaths@Init: PairPath [_paths=[[0, 104, 115, 128], [128]]]=3 PairPaths@Init: PairPath [_paths=[[0, 104, 115, 128], []]]=1 PairPaths@Init: PairPath [_paths=[[0], [115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [0, 104, 115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0], [0, 337]]]=3 PairPaths@Init: PairPath [_paths=[[0], [104, 115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0], [0, 104, 115, 128]]]=2 PairPaths@Init: PairPath [_paths=[[0, 104], []]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115, 128], [115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104], [0, 104, 115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 337], [337, 128]]]=4 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [361, 115, 128]]]=1 Start Vertex:128 PairPaths@Init: PairPath [_paths=[[128], [128]]]=24 PairPaths@Init: PairPath [_paths=[[128], []]]=16 Start Vertex:337 PairPaths@Init: PairPath [_paths=[[337, 128], [337, 128]]]=1 PairPaths@Init: PairPath [_paths=[[337, 128], [128]]]=1 Start Vertex:115 PairPaths@Init: PairPath [_paths=[[115, 128], [128]]]=2 SECTION ======== Create DAG from Overlap Layout ============ Noncontained paths: [[0, 104, 115, 128], [361, 115, 128], [337, 128], [0, 337]] Node[128] has repeat count: 3 Node[0] has repeat count: 2 Node[337] has repeat count: 2 Node[115] has repeat count: 2 Node[104] has repeat count: 1 Node[361] has repeat count: 1 path PN1::[0, 104, 115, 128] extends no path path PN2::[361, 115, 128] extends no path PathNode Overlap Detected: [overlap: 1] PN4::[0, 337] extended by PN3::[337, 128] extension of: PN4::[0, 337] by PN3::[337, 128] has 1 terminal matches. path PN4::[0, 337] extends no path PathNodeDescription: PN1::[0, 104, 115, 128] PathNodeDescription: PN3::[337, 128] PathNodeDescription: PN2::[361, 115, 128] PathNodeDescription: PN4::[0, 337] // Breaking cycles in Path Overlap Graph (POG), Round: 1 SECTION ======== Convert Path-DAG to SeqVertex-DAG ============ prep_for_DAG_collapse: PN1 CurrVert:[385, 386, 387, 388], OrigVert:[0, 104, 115, 128] prep_for_DAG_collapse: PN3 CurrVert:[389, 390], OrigVert:[337, 128] prep_for_DAG_collapse: PN2 CurrVert:[391, 392, 393], OrigVert:[361, 115, 128] prep_for_DAG_collapse: PN4 CurrVert:[394, 395], OrigVert:[0, 337] DFS_path_to_graph: targeting: PN1::[0, 104, 115, 128] DFS_path_to_graph: targeting: PN2::[361, 115, 128] DFS_path_to_graph: targeting: PN4::[0, 337] DFS_path_to_graph: targeting: PN3::[337, 128] ## Round: 1 Zipping up. ## zip_up() attempt_zip_merge_SeqVertices([AACATTTTTG...GATATTCTTT:W5(V389_337_D1), TCAGAACAGTCATTGATATTCTTT:W5(V395_337_D6)]) UpZipMerging nodes: [AACATTTTTG...GATATTCTTT:W5(V389_337_D1), AACATTTTTG...GATATTCTTT:W5(V395_337_D6)] to TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) Zip up merged: 2 nodes. ## Round: 2 Zipping up. Zip up merged: 0 nodes. ## Round: 3 Zipping down. Zip down merged: 0 nodes. ## Round: 4 Zipping up. Zip up merged: 0 nodes. ## Round: 5 Zipping down. Zip down merged: 0 nodes. Old_to_new_vertex_id_mapping: 385 => 385 (stays same) Old_to_new_vertex_id_mapping: 391 => 391 (stays same) Old_to_new_vertex_id_mapping: 394 => 394 (stays same) Old_to_new_vertex_id_mapping: 386 => 386 (stays same) Old_to_new_vertex_id_mapping: 392 => 392 (stays same) Old_to_new_vertex_id_mapping: 389 => 396 Old_to_new_vertex_id_mapping: 395 => 396 Old_to_new_vertex_id_mapping: 387 => 387 (stays same) Old_to_new_vertex_id_mapping: 393 => 393 (stays same) Old_to_new_vertex_id_mapping: 390 => 390 (stays same) Old_to_new_vertex_id_mapping: 388 => 388 (stays same) Old-to-new-path mappings: {[337, 128]=[396, 390], [361, 115, 128]=[391, 392, 393], [0, 337]=[394, 396], [0, 104, 115, 128]=[385, 386, 387, 388]} LONG_READ_PATH_MAP is:{} LONG_READ_NAME_TO_PPath is : {} LONG_READ_PATH_MAP updated to:{} LONG_READ_NAME_TO_PPath updated to : {} Printing Pair Paths ------------------ Start Vertex:385 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385, 386, 387, 388]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], []]]=11 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [387, 388]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [392, 393]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [394, 396]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [386, 387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [393]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], [392, 393]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [390]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], [385, 386, 387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [391, 392, 393]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385, 386]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [392, 393]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [392, 393]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], []]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], [387, 388]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385, 386, 387]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [385, 386, 387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [394]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [390]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], []]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [388]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [393]]]=3 Start Vertex:387 PairPaths@PostOverlapLayout: PairPath [_paths=[[387, 388], [393]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[387, 388], [390]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[387, 388], [388]]]=2 Start Vertex:388 PairPaths@PostOverlapLayout: PairPath [_paths=[[388], [388]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[388], [390]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[388], [393]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[388], []]]=16 Start Vertex:390 PairPaths@PostOverlapLayout: PairPath [_paths=[[390], [390]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[390], [393]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[390], []]]=16 PairPaths@PostOverlapLayout: PairPath [_paths=[[390], [388]]]=24 Start Vertex:392 PairPaths@PostOverlapLayout: PairPath [_paths=[[392, 393], [393]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[392, 393], [390]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[392, 393], [388]]]=2 Start Vertex:393 PairPaths@PostOverlapLayout: PairPath [_paths=[[393], [393]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[393], []]]=16 PairPaths@PostOverlapLayout: PairPath [_paths=[[393], [388]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[393], [390]]]=24 Start Vertex:394 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [394]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [385]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], []]]=11 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [392, 393]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [385, 386]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [385, 386, 387, 388]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [394, 396]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [385, 386, 387]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[394, 396], [396, 390]]]=4 PairPaths@PostOverlapLayout: PairPath [_paths=[[394], [386, 387, 388]]]=1 Start Vertex:396 PairPaths@PostOverlapLayout: PairPath [_paths=[[396, 390], [396, 390]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[396, 390], [393]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[396, 390], [390]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[396, 390], [388]]]=1 SECTION ======= Reorganize Read Pairings ========= NODE_DESCR: TAAAGGGGAT...GTTTGATGAA:W21(V385_0_D0) Preds: [] Succ: [CCAGAACAGTC:W21(V386_104_D1) ] NODE_DESCR: CCAGAACAGTC:W21(V386_104_D1) Preds: [TAAAGGGGAT...GTTTGATGAA:W21(V385_0_D0) ] Succ: [ATTGATATTCTTT:W17(V387_115_D2) ] NODE_DESCR: ATTGATATTCTTT:W17(V387_115_D2) Preds: [CCAGAACAGTC:W21(V386_104_D1) ] Succ: [ATAAGCATAT...TATGCTTGTG:W20(V388_128_D3) ] NODE_DESCR: ATAAGCATAT...TATGCTTGTG:W20(V388_128_D3) Preds: [ATTGATATTCTTT:W17(V387_115_D2) ] Succ: [] NODE_DESCR: ATAAGCATAT...TATGCTTGTG:W20(V390_128_D2) Preds: [TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) ] Succ: [] NODE_DESCR: TCATGGCTGA...CAGAACAGTC:W2(V391_361_D0) Preds: [] Succ: [ATTGATATTCTTT:W17(V392_115_D1) ] NODE_DESCR: ATTGATATTCTTT:W17(V392_115_D1) Preds: [TCATGGCTGA...CAGAACAGTC:W2(V391_361_D0) ] Succ: [ATAAGCATAT...TATGCTTGTG:W20(V393_128_D2) ] NODE_DESCR: ATAAGCATAT...TATGCTTGTG:W20(V393_128_D2) Preds: [ATTGATATTCTTT:W17(V392_115_D1) ] Succ: [] NODE_DESCR: TAAAGGGGAT...GTTTGATGAA:W21(V394_0_D0) Preds: [] Succ: [TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) ] NODE_DESCR: TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) Preds: [TAAAGGGGAT...GTTTGATGAA:W21(V394_0_D0) ] Succ: [ATAAGCATAT...TATGCTTGTG:W20(V390_128_D2) ] combinePaths: [385, 386, 387], [388] Could Impute path connectingPairPath [_paths=[[385, 386, 387], [388]]] containing intervening nodes: [] we have 1 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387], [388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [385, 386, 387, 388] we have 3 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385, 386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] we have 11 reads supporting the path: PairPath [_paths=[[385], []]] combinePaths: [385, 386, 387], [387, 388] we have 6 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [392, 393] we have 12 reads supporting the path: PairPath [_paths=[[385], []]] we have 1 reads supporting the path: PairPath [_paths=[[392, 393], []]] Warning... pp: PairPath [_paths=[[385], [392, 393]]] needed to be split into: PairPath [_paths=[[385], []]] and PairPath [_paths=[[392, 393], []]] combinePaths: [385], [394, 396] we have 15 reads supporting the path: PairPath [_paths=[[385], []]] we have 3 reads supporting the path: PairPath [_paths=[[394, 396], []]] Warning... pp: PairPath [_paths=[[385], [394, 396]]] needed to be split into: PairPath [_paths=[[385], []]] and PairPath [_paths=[[394, 396], []]] combinePaths: [385], [386, 387, 388] Could Impute path connectingPairPath [_paths=[[385], [386, 387, 388]]] containing intervening nodes: [] we have 7 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385], [386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387, 388], [387, 388] we have 8 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387, 388], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387], [393] we have 1 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] we have 1 reads supporting the path: PairPath [_paths=[[393], []]] Warning... pp: PairPath [_paths=[[385, 386, 387], [393]]] needed to be split into: PairPath [_paths=[[385, 386, 387], []]] and PairPath [_paths=[[393], []]] combinePaths: [385, 386], [392, 393] we have 3 reads supporting the path: PairPath [_paths=[[385, 386], []]] we have 4 reads supporting the path: PairPath [_paths=[[392, 393], []]] Warning... pp: PairPath [_paths=[[385, 386], [392, 393]]] needed to be split into: PairPath [_paths=[[385, 386], []]] and PairPath [_paths=[[392, 393], []]] combinePaths: [385, 386, 387], [390] we have 2 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] we have 1 reads supporting the path: PairPath [_paths=[[390], []]] Warning... pp: PairPath [_paths=[[385, 386, 387], [390]]] needed to be split into: PairPath [_paths=[[385, 386, 387], []]] and PairPath [_paths=[[390], []]] combinePaths: [385, 386], [385, 386, 387, 388] we have 9 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386], [385, 386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387], [391, 392, 393] we have 3 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] we have 1 reads supporting the path: PairPath [_paths=[[391, 392, 393], []]] Warning... pp: PairPath [_paths=[[385, 386, 387], [391, 392, 393]]] needed to be split into: PairPath [_paths=[[385, 386, 387], []]] and PairPath [_paths=[[391, 392, 393], []]] combinePaths: [385], [385] we have 21 reads supporting the path: PairPath [_paths=[[385], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385]]] => PairPath [_paths=[[385], []]] combinePaths: [385], [385, 386] we have 9 reads supporting the path: PairPath [_paths=[[385, 386], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385, 386]]] => PairPath [_paths=[[385, 386], []]] combinePaths: [385, 386, 387], [392, 393] we have 6 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] we have 7 reads supporting the path: PairPath [_paths=[[392, 393], []]] Warning... pp: PairPath [_paths=[[385, 386, 387], [392, 393]]] needed to be split into: PairPath [_paths=[[385, 386, 387], []]] and PairPath [_paths=[[392, 393], []]] combinePaths: [385], [387, 388] Could Impute path connectingPairPath [_paths=[[385], [387, 388]]] containing intervening nodes: [386] we have 10 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387, 388], [392, 393] we have 11 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] we have 8 reads supporting the path: PairPath [_paths=[[392, 393], []]] Warning... pp: PairPath [_paths=[[385, 386, 387, 388], [392, 393]]] needed to be split into: PairPath [_paths=[[385, 386, 387, 388], []]] and PairPath [_paths=[[392, 393], []]] we have 12 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386], [387, 388] Could Impute path connectingPairPath [_paths=[[385, 386], [387, 388]]] containing intervening nodes: [] we have 15 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [385, 386, 387] we have 8 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385, 386, 387]]] => PairPath [_paths=[[385, 386, 387], []]] combinePaths: [385, 386, 387], [385, 386, 387, 388] we have 16 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387], [385, 386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [394] we have 27 reads supporting the path: PairPath [_paths=[[385], []]] we have 6 reads supporting the path: PairPath [_paths=[[394], []]] Warning... pp: PairPath [_paths=[[385], [394]]] needed to be split into: PairPath [_paths=[[385], []]] and PairPath [_paths=[[394], []]] combinePaths: [385, 386, 387, 388], [390] we have 19 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] we have 4 reads supporting the path: PairPath [_paths=[[390], []]] Warning... pp: PairPath [_paths=[[385, 386, 387, 388], [390]]] needed to be split into: PairPath [_paths=[[385, 386, 387, 388], []]] and PairPath [_paths=[[390], []]] we have 10 reads supporting the path: PairPath [_paths=[[385, 386], []]] combinePaths: [385, 386, 387, 388], [388] we have 22 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387, 388], [388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387, 388], [393] we have 25 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] we have 4 reads supporting the path: PairPath [_paths=[[393], []]] Warning... pp: PairPath [_paths=[[385, 386, 387, 388], [393]]] needed to be split into: PairPath [_paths=[[385, 386, 387, 388], []]] and PairPath [_paths=[[393], []]] combinePaths: [387, 388], [393] we have 2 reads supporting the path: PairPath [_paths=[[387, 388], []]] we have 6 reads supporting the path: PairPath [_paths=[[393], []]] Warning... pp: PairPath [_paths=[[387, 388], [393]]] needed to be split into: PairPath [_paths=[[387, 388], []]] and PairPath [_paths=[[393], []]] combinePaths: [387, 388], [390] we have 4 reads supporting the path: PairPath [_paths=[[387, 388], []]] we have 6 reads supporting the path: PairPath [_paths=[[390], []]] Warning... pp: PairPath [_paths=[[387, 388], [390]]] needed to be split into: PairPath [_paths=[[387, 388], []]] and PairPath [_paths=[[390], []]] combinePaths: [387, 388], [388] we have 6 reads supporting the path: PairPath [_paths=[[387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[387, 388], [388]]] => PairPath [_paths=[[387, 388], []]] combinePaths: [388], [388] we have 24 reads supporting the path: PairPath [_paths=[[388], []]] OK pp update to new DAG: PairPath [_paths=[[388], [388]]] => PairPath [_paths=[[388], []]] combinePaths: [388], [390] we have 48 reads supporting the path: PairPath [_paths=[[388], []]] we have 30 reads supporting the path: PairPath [_paths=[[390], []]] Warning... pp: PairPath [_paths=[[388], [390]]] needed to be split into: PairPath [_paths=[[388], []]] and PairPath [_paths=[[390], []]] combinePaths: [388], [393] we have 72 reads supporting the path: PairPath [_paths=[[388], []]] we have 30 reads supporting the path: PairPath [_paths=[[393], []]] Warning... pp: PairPath [_paths=[[388], [393]]] needed to be split into: PairPath [_paths=[[388], []]] and PairPath [_paths=[[393], []]] we have 88 reads supporting the path: PairPath [_paths=[[388], []]] combinePaths: [390], [390] we have 54 reads supporting the path: PairPath [_paths=[[390], []]] OK pp update to new DAG: PairPath [_paths=[[390], [390]]] => PairPath [_paths=[[390], []]] combinePaths: [390], [393] we have 78 reads supporting the path: PairPath [_paths=[[390], []]] we have 54 reads supporting the path: PairPath [_paths=[[393], []]] Warning... pp: PairPath [_paths=[[390], [393]]] needed to be split into: PairPath [_paths=[[390], []]] and PairPath [_paths=[[393], []]] we have 94 reads supporting the path: PairPath [_paths=[[390], []]] combinePaths: [390], [388] we have 118 reads supporting the path: PairPath [_paths=[[390], []]] we have 112 reads supporting the path: PairPath [_paths=[[388], []]] Warning... pp: PairPath [_paths=[[390], [388]]] needed to be split into: PairPath [_paths=[[390], []]] and PairPath [_paths=[[388], []]] combinePaths: [392, 393], [393] we have 10 reads supporting the path: PairPath [_paths=[[392, 393], []]] OK pp update to new DAG: PairPath [_paths=[[392, 393], [393]]] => PairPath [_paths=[[392, 393], []]] combinePaths: [392, 393], [390] we have 12 reads supporting the path: PairPath [_paths=[[392, 393], []]] we have 120 reads supporting the path: PairPath [_paths=[[390], []]] Warning... pp: PairPath [_paths=[[392, 393], [390]]] needed to be split into: PairPath [_paths=[[392, 393], []]] and PairPath [_paths=[[390], []]] combinePaths: [392, 393], [388] we have 14 reads supporting the path: PairPath [_paths=[[392, 393], []]] we have 114 reads supporting the path: PairPath [_paths=[[388], []]] Warning... pp: PairPath [_paths=[[392, 393], [388]]] needed to be split into: PairPath [_paths=[[392, 393], []]] and PairPath [_paths=[[388], []]] combinePaths: [393], [393] we have 78 reads supporting the path: PairPath [_paths=[[393], []]] OK pp update to new DAG: PairPath [_paths=[[393], [393]]] => PairPath [_paths=[[393], []]] we have 94 reads supporting the path: PairPath [_paths=[[393], []]] combinePaths: [393], [388] we have 118 reads supporting the path: PairPath [_paths=[[393], []]] we have 138 reads supporting the path: PairPath [_paths=[[388], []]] Warning... pp: PairPath [_paths=[[393], [388]]] needed to be split into: PairPath [_paths=[[393], []]] and PairPath [_paths=[[388], []]] combinePaths: [393], [390] we have 142 reads supporting the path: PairPath [_paths=[[393], []]] we have 144 reads supporting the path: PairPath [_paths=[[390], []]] Warning... pp: PairPath [_paths=[[393], [390]]] needed to be split into: PairPath [_paths=[[393], []]] and PairPath [_paths=[[390], []]] combinePaths: [394], [394] we have 12 reads supporting the path: PairPath [_paths=[[394], []]] OK pp update to new DAG: PairPath [_paths=[[394], [394]]] => PairPath [_paths=[[394], []]] combinePaths: [394], [385] we have 18 reads supporting the path: PairPath [_paths=[[394], []]] we have 33 reads supporting the path: PairPath [_paths=[[385], []]] Warning... pp: PairPath [_paths=[[394], [385]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[385], []]] we have 29 reads supporting the path: PairPath [_paths=[[394], []]] combinePaths: [394], [392, 393] we have 30 reads supporting the path: PairPath [_paths=[[394], []]] we have 15 reads supporting the path: PairPath [_paths=[[392, 393], []]] Warning... pp: PairPath [_paths=[[394], [392, 393]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[392, 393], []]] combinePaths: [394], [385, 386] we have 36 reads supporting the path: PairPath [_paths=[[394], []]] we have 16 reads supporting the path: PairPath [_paths=[[385, 386], []]] Warning... pp: PairPath [_paths=[[394], [385, 386]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[385, 386], []]] combinePaths: [394], [385, 386, 387, 388] we have 38 reads supporting the path: PairPath [_paths=[[394], []]] we have 27 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] Warning... pp: PairPath [_paths=[[394], [385, 386, 387, 388]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [394], [387, 388] we have 39 reads supporting the path: PairPath [_paths=[[394], []]] we have 7 reads supporting the path: PairPath [_paths=[[387, 388], []]] Warning... pp: PairPath [_paths=[[394], [387, 388]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[387, 388], []]] combinePaths: [394], [394, 396] we have 6 reads supporting the path: PairPath [_paths=[[394, 396], []]] OK pp update to new DAG: PairPath [_paths=[[394], [394, 396]]] => PairPath [_paths=[[394, 396], []]] combinePaths: [394], [385, 386, 387] we have 41 reads supporting the path: PairPath [_paths=[[394], []]] we have 10 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] Warning... pp: PairPath [_paths=[[394], [385, 386, 387]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[385, 386, 387], []]] combinePaths: [394, 396], [396, 390] we have 4 reads supporting the path: PairPath [_paths=[[394, 396, 390], []]] OK pp update to new DAG: PairPath [_paths=[[394, 396], [396, 390]]] => PairPath [_paths=[[394, 396, 390], []]] combinePaths: [394], [386, 387, 388] we have 42 reads supporting the path: PairPath [_paths=[[394], []]] we have 1 reads supporting the path: PairPath [_paths=[[386, 387, 388], []]] Warning... pp: PairPath [_paths=[[394], [386, 387, 388]]] needed to be split into: PairPath [_paths=[[394], []]] and PairPath [_paths=[[386, 387, 388], []]] combinePaths: [396, 390], [396, 390] we have 1 reads supporting the path: PairPath [_paths=[[396, 390], []]] OK pp update to new DAG: PairPath [_paths=[[396, 390], [396, 390]]] => PairPath [_paths=[[396, 390], []]] combinePaths: [396, 390], [393] we have 2 reads supporting the path: PairPath [_paths=[[396, 390], []]] we have 143 reads supporting the path: PairPath [_paths=[[393], []]] Warning... pp: PairPath [_paths=[[396, 390], [393]]] needed to be split into: PairPath [_paths=[[396, 390], []]] and PairPath [_paths=[[393], []]] combinePaths: [396, 390], [390] we have 3 reads supporting the path: PairPath [_paths=[[396, 390], []]] OK pp update to new DAG: PairPath [_paths=[[396, 390], [390]]] => PairPath [_paths=[[396, 390], []]] combinePaths: [396, 390], [388] we have 4 reads supporting the path: PairPath [_paths=[[396, 390], []]] we have 139 reads supporting the path: PairPath [_paths=[[388], []]] Warning... pp: PairPath [_paths=[[396, 390], [388]]] needed to be split into: PairPath [_paths=[[396, 390], []]] and PairPath [_paths=[[388], []]] Start Vertex:385 PairPaths@AfterPairReorganization: PairPath [_paths=[[385], []]]=33 PairPaths@AfterPairReorganization: PairPath [_paths=[[385, 386, 387], []]]=10 PairPaths@AfterPairReorganization: PairPath [_paths=[[385, 386, 387, 388], []]]=27 PairPaths@AfterPairReorganization: PairPath [_paths=[[385, 386], []]]=16 Start Vertex:386 PairPaths@AfterPairReorganization: PairPath [_paths=[[386, 387, 388], []]]=1 Start Vertex:387 PairPaths@AfterPairReorganization: PairPath [_paths=[[387, 388], []]]=7 Start Vertex:388 PairPaths@AfterPairReorganization: PairPath [_paths=[[388], []]]=139 Start Vertex:390 PairPaths@AfterPairReorganization: PairPath [_paths=[[390], []]]=144 Start Vertex:391 PairPaths@AfterPairReorganization: PairPath [_paths=[[391, 392, 393], []]]=1 Start Vertex:392 PairPaths@AfterPairReorganization: PairPath [_paths=[[392, 393], []]]=15 Start Vertex:393 PairPaths@AfterPairReorganization: PairPath [_paths=[[393], []]]=143 Start Vertex:394 PairPaths@AfterPairReorganization: PairPath [_paths=[[394, 396], []]]=6 PairPaths@AfterPairReorganization: PairPath [_paths=[[394], []]]=42 PairPaths@AfterPairReorganization: PairPath [_paths=[[394, 396, 390], []]]=4 Start Vertex:396 PairPaths@AfterPairReorganization: PairPath [_paths=[[396, 390], []]]=4 ComponentDivision: 0 contains the following vertices: node_id: 391 node_id: 392 node_id: 393 ComponentDivision: 1 contains the following vertices: node_id: 385 node_id: 386 node_id: 387 node_id: 388 ComponentDivision: 2 contains the following vertices: node_id: 390 node_id: 394 node_id: 396 total number of components = 3 Searching for kmer set: CCAGAACAGTCATTGATATTCTTT -> CAGAACAGTCATTGATATTCTTTA Searching for kmer set: ATGGTTTGATGAACCAGAACAGTC -> TGGTTTGATGAACCAGAACAGTCA Searching for kmer set: GTGGTTTGATGAACCAGAACAGTC -> TGGTTTGATGAACCAGAACAGTCA Searching for kmer set: AAACATTTTTGATGGTTTGATGAA -> AACATTTTTGATGGTTTGATGAAT Searching for kmer set: TCAGAACAGTCATTGATATTCTTT -> CAGAACAGTCATTGATATTCTTTA Searching for kmer set: AAACATTTTTGATGGTTTGATGAA -> AACATTTTTGATGGTTTGATGAAC Searching for kmer set: CCAGAACAGTCATTGATATTCTTT -> CAGAACAGTCATTGATATTCTTTA SECTION ============= Begin Assembly =============== Assembling subcomponent 0 Subcomponent: 0, adding pairpath: PairPath [_paths=[[391, 392, 393], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[392, 393], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[393], []]] #### Component Read Summary BEFORE PairPath-per-node Reduction ***** PairPath Counts ***** componentReadHash, start node: 391 has size: 1 Node: 391 has 1 pairpaths stored: PairPath [_paths=[[391, 392, 393], []]] has read support: 1 componentReadHash, start node: 392 has size: 1 Node: 392 has 1 pairpaths stored: PairPath [_paths=[[392, 393], []]] has read support: 15 componentReadHash, start node: 393 has size: 1 Node: 393 has 1 pairpaths stored: PairPath [_paths=[[393], []]] has read support: 143 ## Total number of pairpaths: 3 #### Component Read Summary AFTER PairPath-per-node Reduction ***** PairPath Counts ***** componentReadHash, start node: 391 has size: 1 Node: 391 has 1 pairpaths stored: PairPath [_paths=[[391, 392, 393], []]] has read support: 1 componentReadHash, start node: 392 has size: 1 Node: 392 has 1 pairpaths stored: PairPath [_paths=[[392, 393], []]] has read support: 15 componentReadHash, start node: 393 has size: 1 Node: 393 has 1 pairpaths stored: PairPath [_paths=[[393], []]] has read support: 143 ## Total number of pairpaths: 3 ### Extracting triplets from reads. Setting initial triplet adjacency_path for central node: 392 => [391, 392, 393] ### 1 nodes have locked-in triplet paths: Triplet locks for: 392 : [[391, 392, 393]] ### Extracting complex path prefixes from reads. -capturing path prefixes -removing prefixes that are subpaths of other prefixes EXTENDED_TRIPLET_CAPTURED: [391, 392, 393] #### Extended triplets from reads: Complex prefix paths for: 393 : [[391, 392, 393]] SECTION ############### ## Starting Butterfly Assembly ## ################### PairPaths to assemble: Start Vertex:-1 PairPaths@BflyStart: PairPath [_paths=[[-1, 391], []]]=1 Start Vertex:391 PairPaths@BflyStart: PairPath [_paths=[[391, 392, 393], []]]=1 Start Vertex:392 PairPaths@BflyStart: PairPath [_paths=[[392, 393], []]]=15 Start Vertex:393 PairPaths@BflyStart: PairPath [_paths=[[393], []]]=143 PairPaths@BflyStart: PairPath [_paths=[[393, -2], []]]=1 QUEUE IS: [:W2147483647(V-1_D-1)] #### getAllProbablePaths() The next node in the queue C is -1 butterfly pct done: 1 / 3 = 33.333336% pct done. ReadsStartingAtV_START_BFLY, Node: -1 read: PairPath [_paths=[[-1, 391], []]] Exploring extension of: 1 paths that end at vertex: -1 == Current Paths Constructed Up To Vertex: -1 : PathPartialReconstruction@[-1] : [-1] Adding the reads {PairPath [_paths=[[-1, 391], []]]=1} to the path [-1] ################################################ ###### Exploring extension of v: -1 by successor: 391 ################################################ Count of paths ending at v: -1 = 1 path_ending_at_v: [-1] # [PathCounter(391)=0 Examining potential extension of path ending at node V: -1 by successor: 391, via path=[-1] path [-1] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] -checking if subPath has enough read support. Exploring sub path: [-1, 391] -readsOfPathUntilV: PairPath [_paths=[[-1, 391], []]] -checking if pp: PairPath [_paths=[[-1, 391], []]] supports extension of [-1, 391] => true examining subPath: [-1, 391] for reinforcement by read: [[-1, 391], []] :true the read PairPath [_paths=[[-1, 391], []]](1) enforces the sub-path ([-1, 391]) -found: 1 reads supporting subpath. the sub-path ([-1, 391]) has PASSED Successful extension of 391 to generate path [-1, 391] updateReadsOfPath: [-1, 391] read PairPath [_paths=[[-1, 391], []]] is consistent with 391 pct_contained_propagated: 0.0% 391 was added to the queue QUEUE IS: [GTGGTTTGATGAACCAGAACAGTC:W2(V391_361_D0)] #### getAllProbablePaths() The next node in the queue C is 391 butterfly pct done: 2 / 3 = 66.66667% pct done. ReadsStartingAtV_START_BFLY, Node: 391 read: PairPath [_paths=[[391, 392, 393], []]] Exploring extension of: 1 paths that end at vertex: 391 == Current Paths Constructed Up To Vertex: 391 : PathPartialReconstruction@[391] : [-1, 391] Adding the reads {PairPath [_paths=[[391, 392, 393], []]]=1} to the path [-1, 391] ################################################ ###### Exploring extension of v: 391 by successor: 392 ################################################ Count of paths ending at v: 391 = 1 path_ending_at_v: [-1, 391] # [PathCounter(392)=0 Examining potential extension of path ending at node V: 391 by successor: 392, via path=[-1, 391] path [-1, 391] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1, 391] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 392, 393], []]] -checking if subPath has enough read support. Exploring sub path: [-1, 391, 392] -readsOfPathUntilV: PairPath [_paths=[[-1, 391], []]] -checking if pp: PairPath [_paths=[[-1, 391], []]] supports extension of [-1, 391, 392] => false examining subPath: [-1, 391, 392] for reinforcement by read: [[-1, 391], []] :false the read PairPath [_paths=[[-1, 391], []]](1) does not enforce the sub-path ([-1, 391, 392]) -readsOfPathUntilV: PairPath [_paths=[[391, 392, 393], []]] -checking if pp: PairPath [_paths=[[391, 392, 393], []]] supports extension of [-1, 391, 392] => true examining subPath: [-1, 391, 392] for reinforcement by read: [[391, 392, 393], []] :true the read PairPath [_paths=[[391, 392, 393], []]](1) enforces the sub-path ([-1, 391, 392]) -found: 1 reads supporting subpath. the sub-path ([-1, 391, 392]) has PASSED Successful extension of 392 to generate path [-1, 391, 392] updateReadsOfPath: [-1, 391, 392] read PairPath [_paths=[[391, 392, 393], []]] is consistent with 392 pct_contained_propagated: 50.0% 392 was added to the queue QUEUE IS: [ATTGATATTCTTT:W17(V392_115_D1)] #### getAllProbablePaths() The next node in the queue C is 392 butterfly pct done: 3 / 3 = 100.0% pct done. ReadsStartingAtV_START_BFLY, Node: 392 read: PairPath [_paths=[[392, 393], []]] Exploring extension of: 1 paths that end at vertex: 392 == Current Paths Constructed Up To Vertex: 392 : PathPartialReconstruction@[392] : [-1, 391, 392] Adding the reads {PairPath [_paths=[[392, 393], []]]=15} to the path [-1, 391, 392] ################################################ ###### Exploring extension of v: 392 by successor: 393 ################################################ Count of paths ending at v: 392 = 1 path_ending_at_v: [-1, 391, 392] # [PathCounter(393)=0 Examining potential extension of path ending at node V: 392 by successor: 393, via path=[-1, 391, 392] TripletMapper doesnt contain node: 392 ReadsOfPathUntilV: PATH: [-1, 391, 392] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[392, 393], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 392, 393], []]] -checking if subPath has enough read support. Exploring sub path: [393] -readsOfPathUntilV: PairPath [_paths=[[-1, 391], []]] -checking if pp: PairPath [_paths=[[-1, 391], []]] supports extension of [-1, 391, 392, 393] => false examining subPath: [393] for reinforcement by read: [[-1, 391], []] :false the read PairPath [_paths=[[-1, 391], []]](1) does not enforce the sub-path ([393]) -readsOfPathUntilV: PairPath [_paths=[[392, 393], []]] -checking if pp: PairPath [_paths=[[392, 393], []]] supports extension of [-1, 391, 392, 393] => true examining subPath: [393] for reinforcement by read: [[392, 393], []] :true the read PairPath [_paths=[[392, 393], []]](15) enforces the sub-path ([393]) -found: 15 reads supporting subpath. the sub-path ([393]) has PASSED Successful extension of 393 to generate path [-1, 391, 392, 393] updateReadsOfPath: [-1, 391, 392, 393] read PairPath [_paths=[[392, 393], []]] is consistent with 393 read PairPath [_paths=[[391, 392, 393], []]] is consistent with 393 pct_contained_propagated: 33.333336% 393 was added to the queue QUEUE IS: [ATAAGCATAT...TATGCTTGTG:W20(V393_128_D2)] #### getAllProbablePaths() The next node in the queue C is 393 butterfly pct done: 4 / 3 = 133.33334% pct done. ReadsStartingAtV_START_BFLY, Node: 393 read: PairPath [_paths=[[393], []]] ReadsStartingAtV_START_BFLY, Node: 393 read: PairPath [_paths=[[393, -2], []]] Exploring extension of: 1 paths that end at vertex: 393 == Current Paths Constructed Up To Vertex: 393 : PathPartialReconstruction@[393] : [-1, 391, 392, 393] Adding the reads {PairPath [_paths=[[393], []]]=143, PairPath [_paths=[[393, -2], []]]=1} to the path [-1, 391, 392, 393] ################################################ ###### Exploring extension of v: 393 by successor: -2 ################################################ Count of paths ending at v: 393 = 1 path_ending_at_v: [-1, 391, 392, 393] # [PathCounter(-2)=0 Examining potential extension of path ending at node V: 393 by successor: -2, via path=[-1, 391, 392, 393] TripletMapper doesnt contain node: 393 ReadsOfPathUntilV: PATH: [-1, 391, 392, 393] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[392, 393], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[393], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[393, -2], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 392, 393], []]] -checking if subPath has enough read support. Exploring sub path: [393, -2] -readsOfPathUntilV: PairPath [_paths=[[-1, 391], []]] -checking if pp: PairPath [_paths=[[-1, 391], []]] supports extension of [-1, 391, 392, 393, -2] => false examining subPath: [393, -2] for reinforcement by read: [[-1, 391], []] :false the read PairPath [_paths=[[-1, 391], []]](1) does not enforce the sub-path ([393, -2]) -readsOfPathUntilV: PairPath [_paths=[[392, 393], []]] -checking if pp: PairPath [_paths=[[392, 393], []]] supports extension of [-1, 391, 392, 393, -2] => false examining subPath: [393, -2] for reinforcement by read: [[392, 393], []] :false the read PairPath [_paths=[[392, 393], []]](15) does not enforce the sub-path ([393, -2]) -readsOfPathUntilV: PairPath [_paths=[[393], []]] -checking if pp: PairPath [_paths=[[393], []]] supports extension of [-1, 391, 392, 393, -2] => false examining subPath: [393, -2] for reinforcement by read: [[393], []] :false the read PairPath [_paths=[[393], []]](143) does not enforce the sub-path ([393, -2]) -readsOfPathUntilV: PairPath [_paths=[[393, -2], []]] -checking if pp: PairPath [_paths=[[393, -2], []]] supports extension of [-1, 391, 392, 393, -2] => true examining subPath: [393, -2] for reinforcement by read: [[393, -2], []] :true the read PairPath [_paths=[[393, -2], []]](1) enforces the sub-path ([393, -2]) -found: 1 reads supporting subpath. the sub-path ([393, -2]) has PASSED Successful extension of -2 to generate path [-1, 391, 392, 393, -2] updateReadsOfPath: [-1, 391, 392, 393, -2] read PairPath [_paths=[[393], []]] is consistent with -2 read PairPath [_paths=[[393, -2], []]] is consistent with -2 pct_contained_propagated: 60.000004% -2 was added to the queue QUEUE IS: [:W-1(V-2_D-1)] #### getAllProbablePaths() The next node in the queue C is -2 butterfly pct done: 5 / 3 = 166.66666% pct done. ReadsStartingAtV_START_BFLY-2 EMPTY Exploring extension of: 1 paths that end at vertex: -2 == Current Paths Constructed Up To Vertex: -2 : PathPartialReconstruction@[-2] : [-1, 391, 392, 393, -2] the finished path: [-1, 391, 392, 393, -2] was added to the final paths, with 161 support FinalPath@BeforeFiltering: [-1, 391, 392, 393, -2] Grouping paths into genes IsoformClustering, number of clusters = 0 Sep Gene IDs:{[-1, 391, 392, 393, -2]=1} FinalPath@AfterFiltering: [-1, 391, 392, 393, -2] Final Paths: 1 Final path reported: comp0_g1_i1 len=269 path=[391:0-46 392:47-59 393:60-268] [-1, 391, 392, 393, -2] SECTION ============= Begin Assembly =============== Assembling subcomponent 1 Subcomponent: 1, adding pairpath: PairPath [_paths=[[385], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[385, 386, 387], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[385, 386, 387, 388], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[385, 386], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[386, 387, 388], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[387, 388], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[388], []]] #### Component Read Summary BEFORE PairPath-per-node Reduction ***** PairPath Counts ***** componentReadHash, start node: 385 has size: 4 Node: 385 has 4 pairpaths stored: PairPath [_paths=[[385], []]] has read support: 33 PairPath [_paths=[[385, 386, 387, 388], []]] has read support: 27 PairPath [_paths=[[385, 386], []]] has read support: 16 PairPath [_paths=[[385, 386, 387], []]] has read support: 10 componentReadHash, start node: 386 has size: 1 Node: 386 has 1 pairpaths stored: PairPath [_paths=[[386, 387, 388], []]] has read support: 1 componentReadHash, start node: 387 has size: 1 Node: 387 has 1 pairpaths stored: PairPath [_paths=[[387, 388], []]] has read support: 7 componentReadHash, start node: 388 has size: 1 Node: 388 has 1 pairpaths stored: PairPath [_paths=[[388], []]] has read support: 139 ## Total number of pairpaths: 7 #### Component Read Summary AFTER PairPath-per-node Reduction ***** PairPath Counts ***** componentReadHash, start node: 385 has size: 4 Node: 385 has 4 pairpaths stored: PairPath [_paths=[[385], []]] has read support: 33 PairPath [_paths=[[385, 386, 387, 388], []]] has read support: 27 PairPath [_paths=[[385, 386], []]] has read support: 16 PairPath [_paths=[[385, 386, 387], []]] has read support: 10 componentReadHash, start node: 386 has size: 1 Node: 386 has 1 pairpaths stored: PairPath [_paths=[[386, 387, 388], []]] has read support: 1 componentReadHash, start node: 387 has size: 1 Node: 387 has 1 pairpaths stored: PairPath [_paths=[[387, 388], []]] has read support: 7 componentReadHash, start node: 388 has size: 1 Node: 388 has 1 pairpaths stored: PairPath [_paths=[[388], []]] has read support: 139 ## Total number of pairpaths: 7 ### Extracting triplets from reads. Setting initial triplet adjacency_path for central node: 386 => [385, 386, 387] triplet adjacency_path of node: 386 => [385, 386, 387] already captured. Setting initial triplet adjacency_path for central node: 387 => [386, 387, 388] triplet adjacency_path of node: 387 => [386, 387, 388] already captured. ### 2 nodes have locked-in triplet paths: Triplet locks for: 386 : [[385, 386, 387]] Triplet locks for: 387 : [[386, 387, 388]] ### Extracting complex path prefixes from reads. -capturing path prefixes -removing prefixes that are subpaths of other prefixes EXTENDED_TRIPLET_CAPTURED: [385, 386, 387] EXTENDED_TRIPLET_CAPTURED: [385, 386, 387, 388] #### Extended triplets from reads: Complex prefix paths for: 387 : [[385, 386, 387]] Complex prefix paths for: 388 : [[385, 386, 387, 388]] SECTION ############### ## Starting Butterfly Assembly ## ################### PairPaths to assemble: Start Vertex:-1 PairPaths@BflyStart: PairPath [_paths=[[-1, 385], []]]=1 Start Vertex:385 PairPaths@BflyStart: PairPath [_paths=[[385], []]]=33 PairPaths@BflyStart: PairPath [_paths=[[385, 386, 387], []]]=10 PairPaths@BflyStart: PairPath [_paths=[[385, 386, 387, 388], []]]=27 PairPaths@BflyStart: PairPath [_paths=[[385, 386], []]]=16 Start Vertex:386 PairPaths@BflyStart: PairPath [_paths=[[386, 387, 388], []]]=1 Start Vertex:387 PairPaths@BflyStart: PairPath [_paths=[[387, 388], []]]=7 Start Vertex:388 PairPaths@BflyStart: PairPath [_paths=[[388, -2], []]]=1 PairPaths@BflyStart: PairPath [_paths=[[388], []]]=139 QUEUE IS: [:W2147483647(V-1_D-1)] #### getAllProbablePaths() The next node in the queue C is -1 butterfly pct done: 1 / 4 = 25.0% pct done. ReadsStartingAtV_START_BFLY, Node: -1 read: PairPath [_paths=[[-1, 385], []]] Exploring extension of: 1 paths that end at vertex: -1 == Current Paths Constructed Up To Vertex: -1 : PathPartialReconstruction@[-1] : [-1] Adding the reads {PairPath [_paths=[[-1, 385], []]]=1} to the path [-1] ################################################ ###### Exploring extension of v: -1 by successor: 385 ################################################ Count of paths ending at v: -1 = 1 path_ending_at_v: [-1] # [PathCounter(385)=0 Examining potential extension of path ending at node V: -1 by successor: 385, via path=[-1] path [-1] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] -checking if subPath has enough read support. Exploring sub path: [385] -readsOfPathUntilV: PairPath [_paths=[[-1, 385], []]] -checking if pp: PairPath [_paths=[[-1, 385], []]] supports extension of [-1, 385] => true examining subPath: [385] for reinforcement by read: [[-1, 385], []] :true the read PairPath [_paths=[[-1, 385], []]](1) enforces the sub-path ([385]) -found: 1 reads supporting subpath. the sub-path ([385]) has PASSED Successful extension of 385 to generate path [-1, 385] updateReadsOfPath: [-1, 385] read PairPath [_paths=[[-1, 385], []]] is consistent with 385 pct_contained_propagated: 0.0% 385 was added to the queue ################################################ ###### Exploring extension of v: -1 by successor: 391 ################################################ component either lacks: 391 or at sink QUEUE IS: [GAAGTTCATG...GTTTGATGAA:W21(V385_0_D0)] #### getAllProbablePaths() The next node in the queue C is 385 butterfly pct done: 2 / 4 = 50.0% pct done. ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385], []]] ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385, 386, 387], []]] ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385, 386], []]] Exploring extension of: 1 paths that end at vertex: 385 == Current Paths Constructed Up To Vertex: 385 : PathPartialReconstruction@[385] : [-1, 385] Adding the reads {PairPath [_paths=[[385], []]]=33, PairPath [_paths=[[385, 386, 387], []]]=10, PairPath [_paths=[[385, 386, 387, 388], []]]=27, PairPath [_paths=[[385, 386], []]]=16} to the path [-1, 385] ################################################ ###### Exploring extension of v: 385 by successor: 386 ################################################ Count of paths ending at v: 385 = 1 path_ending_at_v: [-1, 385] # [PathCounter(386)=0 Examining potential extension of path ending at node V: 385 by successor: 386, via path=[-1, 385] path [-1, 385] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1, 385] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] -checking if subPath has enough read support. Exploring sub path: [385, 386] -readsOfPathUntilV: PairPath [_paths=[[385], []]] -checking if pp: PairPath [_paths=[[385], []]] supports extension of [-1, 385, 386] => false examining subPath: [385, 386] for reinforcement by read: [[385], []] :false the read PairPath [_paths=[[385], []]](33) does not enforce the sub-path ([385, 386]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387], []]] -checking if pp: PairPath [_paths=[[385, 386, 387], []]] supports extension of [-1, 385, 386] => true examining subPath: [385, 386] for reinforcement by read: [[385, 386, 387], []] :true the read PairPath [_paths=[[385, 386, 387], []]](10) enforces the sub-path ([385, 386]) -found: 10 reads supporting subpath. the sub-path ([385, 386]) has PASSED Successful extension of 386 to generate path [-1, 385, 386] updateReadsOfPath: [-1, 385, 386] read PairPath [_paths=[[385], []]] is consistent with 386 read PairPath [_paths=[[385, 386, 387], []]] is consistent with 386 read PairPath [_paths=[[385, 386, 387, 388], []]] is consistent with 386 read PairPath [_paths=[[385, 386], []]] is consistent with 386 pct_contained_propagated: 20.0% 386 was added to the queue QUEUE IS: [CCAGAACAGTC:W21(V386_104_D1)] #### getAllProbablePaths() The next node in the queue C is 386 butterfly pct done: 3 / 4 = 75.0% pct done. ReadsStartingAtV_START_BFLY, Node: 386 read: PairPath [_paths=[[386, 387, 388], []]] Exploring extension of: 1 paths that end at vertex: 386 == Current Paths Constructed Up To Vertex: 386 : PathPartialReconstruction@[386] : [-1, 385, 386] Adding the reads {PairPath [_paths=[[386, 387, 388], []]]=1} to the path [-1, 385, 386] ################################################ ###### Exploring extension of v: 386 by successor: 387 ################################################ Count of paths ending at v: 386 = 1 path_ending_at_v: [-1, 385, 386] # [PathCounter(387)=0 Examining potential extension of path ending at node V: 386 by successor: 387, via path=[-1, 385, 386] TripletMapper doesnt contain node: 386 ReadsOfPathUntilV: PATH: [-1, 385, 386] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] -checking if subPath has enough read support. Exploring sub path: [385, 386, 387] -readsOfPathUntilV: PairPath [_paths=[[385], []]] -checking if pp: PairPath [_paths=[[385], []]] supports extension of [-1, 385, 386, 387] => false examining subPath: [385, 386, 387] for reinforcement by read: [[385], []] :false the read PairPath [_paths=[[385], []]](33) does not enforce the sub-path ([385, 386, 387]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387], []]] -checking if pp: PairPath [_paths=[[385, 386, 387], []]] supports extension of [-1, 385, 386, 387] => true examining subPath: [385, 386, 387] for reinforcement by read: [[385, 386, 387], []] :true the read PairPath [_paths=[[385, 386, 387], []]](10) enforces the sub-path ([385, 386, 387]) -found: 10 reads supporting subpath. the sub-path ([385, 386, 387]) has PASSED Successful extension of 387 to generate path [-1, 385, 386, 387] updateReadsOfPath: [-1, 385, 386, 387] read PairPath [_paths=[[385, 386, 387], []]] is consistent with 387 read PairPath [_paths=[[385, 386, 387, 388], []]] is consistent with 387 read PairPath [_paths=[[386, 387, 388], []]] is consistent with 387 pct_contained_propagated: 50.0% 387 was added to the queue QUEUE IS: [ATTGATATTCTTT:W17(V387_115_D2)] #### getAllProbablePaths() The next node in the queue C is 387 butterfly pct done: 4 / 4 = 100.0% pct done. ReadsStartingAtV_START_BFLY, Node: 387 read: PairPath [_paths=[[387, 388], []]] Exploring extension of: 1 paths that end at vertex: 387 == Current Paths Constructed Up To Vertex: 387 : PathPartialReconstruction@[387] : [-1, 385, 386, 387] Adding the reads {PairPath [_paths=[[387, 388], []]]=7} to the path [-1, 385, 386, 387] ################################################ ###### Exploring extension of v: 387 by successor: 388 ################################################ Count of paths ending at v: 387 = 1 path_ending_at_v: [-1, 385, 386, 387] # [PathCounter(388)=0 Examining potential extension of path ending at node V: 387 by successor: 388, via path=[-1, 385, 386, 387] TripletMapper doesnt contain node: 387 ReadsOfPathUntilV: PATH: [-1, 385, 386, 387] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] -checking if subPath has enough read support. Exploring sub path: [388] -readsOfPathUntilV: PairPath [_paths=[[385], []]] -checking if pp: PairPath [_paths=[[385], []]] supports extension of [-1, 385, 386, 387, 388] => false examining subPath: [388] for reinforcement by read: [[385], []] :false the read PairPath [_paths=[[385], []]](33) does not enforce the sub-path ([388]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387], []]] -checking if pp: PairPath [_paths=[[385, 386, 387], []]] supports extension of [-1, 385, 386, 387, 388] => false examining subPath: [388] for reinforcement by read: [[385, 386, 387], []] :false the read PairPath [_paths=[[385, 386, 387], []]](10) does not enforce the sub-path ([388]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387, 388], []]] -checking if pp: PairPath [_paths=[[385, 386, 387, 388], []]] supports extension of [-1, 385, 386, 387, 388] => true examining subPath: [388] for reinforcement by read: [[385, 386, 387, 388], []] :true the read PairPath [_paths=[[385, 386, 387, 388], []]](27) enforces the sub-path ([388]) -found: 27 reads supporting subpath. the sub-path ([388]) has PASSED Successful extension of 388 to generate path [-1, 385, 386, 387, 388] updateReadsOfPath: [-1, 385, 386, 387, 388] read PairPath [_paths=[[385, 386, 387, 388], []]] is consistent with 388 read PairPath [_paths=[[387, 388], []]] is consistent with 388 read PairPath [_paths=[[386, 387, 388], []]] is consistent with 388 pct_contained_propagated: 57.14286% 388 was added to the queue QUEUE IS: [ATAAGCATAT...TATGCTTGTG:W20(V388_128_D3)] #### getAllProbablePaths() The next node in the queue C is 388 butterfly pct done: 5 / 4 = 125.0% pct done. ReadsStartingAtV_START_BFLY, Node: 388 read: PairPath [_paths=[[388, -2], []]] ReadsStartingAtV_START_BFLY, Node: 388 read: PairPath [_paths=[[388], []]] Exploring extension of: 1 paths that end at vertex: 388 == Current Paths Constructed Up To Vertex: 388 : PathPartialReconstruction@[388] : [-1, 385, 386, 387, 388] Adding the reads {PairPath [_paths=[[388, -2], []]]=1, PairPath [_paths=[[388], []]]=139} to the path [-1, 385, 386, 387, 388] ################################################ ###### Exploring extension of v: 388 by successor: -2 ################################################ Count of paths ending at v: 388 = 1 path_ending_at_v: [-1, 385, 386, 387, 388] # [PathCounter(-2)=0 Examining potential extension of path ending at node V: 388 by successor: -2, via path=[-1, 385, 386, 387, 388] TripletMapper doesnt contain node: 388 ReadsOfPathUntilV: PATH: [-1, 385, 386, 387, 388] ReadsOfPathUntiV: READ: PairPath [_paths=[[388, -2], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[388], []]] -checking if subPath has enough read support. Exploring sub path: [388, -2] -readsOfPathUntilV: PairPath [_paths=[[388, -2], []]] -checking if pp: PairPath [_paths=[[388, -2], []]] supports extension of [-1, 385, 386, 387, 388, -2] => true examining subPath: [388, -2] for reinforcement by read: [[388, -2], []] :true the read PairPath [_paths=[[388, -2], []]](1) enforces the sub-path ([388, -2]) -found: 1 reads supporting subpath. the sub-path ([388, -2]) has PASSED Successful extension of -2 to generate path [-1, 385, 386, 387, 388, -2] updateReadsOfPath: [-1, 385, 386, 387, 388, -2] read PairPath [_paths=[[388, -2], []]] is consistent with -2 read PairPath [_paths=[[388], []]] is consistent with -2 pct_contained_propagated: 77.77778% -2 was added to the queue QUEUE IS: [:W-1(V-2_D-1)] #### getAllProbablePaths() The next node in the queue C is -2 butterfly pct done: 6 / 4 = 150.0% pct done. ReadsStartingAtV_START_BFLY-2 EMPTY Exploring extension of: 1 paths that end at vertex: -2 == Current Paths Constructed Up To Vertex: -2 : PathPartialReconstruction@[-2] : [-1, 385, 386, 387, 388, -2] the finished path: [-1, 385, 386, 387, 388, -2] was added to the final paths, with 235 support FinalPath@BeforeFiltering: [-1, 385, 386, 387, 388, -2] Grouping paths into genes IsoformClustering, number of clusters = 0 Sep Gene IDs:{[-1, 385, 386, 387, 388, -2]=1} FinalPath@AfterFiltering: [-1, 385, 386, 387, 388, -2] Final Paths: 1 Final path reported: comp0_g2_i1 len=360 path=[385:0-126 386:127-137 387:138-150 388:151-359] [-1, 385, 386, 387, 388, -2] SECTION ============= Begin Assembly =============== Assembling subcomponent 2 Subcomponent: 2, adding pairpath: PairPath [_paths=[[390], []]] Subcomponent: 2, adding pairpath: PairPath [_paths=[[394, 396], []]] Subcomponent: 2, adding pairpath: PairPath [_paths=[[394], []]] Subcomponent: 2, adding pairpath: PairPath [_paths=[[394, 396, 390], []]] Subcomponent: 2, adding pairpath: PairPath [_paths=[[396, 390], []]] #### Component Read Summary BEFORE PairPath-per-node Reduction ***** PairPath Counts ***** componentReadHash, start node: 390 has size: 1 Node: 390 has 1 pairpaths stored: PairPath [_paths=[[390], []]] has read support: 144 componentReadHash, start node: 394 has size: 3 Node: 394 has 3 pairpaths stored: PairPath [_paths=[[394], []]] has read support: 42 PairPath [_paths=[[394, 396], []]] has read support: 6 PairPath [_paths=[[394, 396, 390], []]] has read support: 4 componentReadHash, start node: 396 has size: 1 Node: 396 has 1 pairpaths stored: PairPath [_paths=[[396, 390], []]] has read support: 4 ## Total number of pairpaths: 5 #### Component Read Summary AFTER PairPath-per-node Reduction ***** PairPath Counts ***** componentReadHash, start node: 390 has size: 1 Node: 390 has 1 pairpaths stored: PairPath [_paths=[[390], []]] has read support: 144 componentReadHash, start node: 394 has size: 3 Node: 394 has 3 pairpaths stored: PairPath [_paths=[[394], []]] has read support: 42 PairPath [_paths=[[394, 396], []]] has read support: 6 PairPath [_paths=[[394, 396, 390], []]] has read support: 4 componentReadHash, start node: 396 has size: 1 Node: 396 has 1 pairpaths stored: PairPath [_paths=[[396, 390], []]] has read support: 4 ## Total number of pairpaths: 5 ### Extracting triplets from reads. Setting initial triplet adjacency_path for central node: 396 => [394, 396, 390] ### 1 nodes have locked-in triplet paths: Triplet locks for: 396 : [[394, 396, 390]] ### Extracting complex path prefixes from reads. -capturing path prefixes -removing prefixes that are subpaths of other prefixes EXTENDED_TRIPLET_CAPTURED: [394, 396, 390] #### Extended triplets from reads: Complex prefix paths for: 390 : [[394, 396, 390]] SECTION ############### ## Starting Butterfly Assembly ## ################### PairPaths to assemble: Start Vertex:-1 PairPaths@BflyStart: PairPath [_paths=[[-1, 394], []]]=1 Start Vertex:390 PairPaths@BflyStart: PairPath [_paths=[[390], []]]=144 PairPaths@BflyStart: PairPath [_paths=[[390, -2], []]]=1 Start Vertex:394 PairPaths@BflyStart: PairPath [_paths=[[394, 396], []]]=6 PairPaths@BflyStart: PairPath [_paths=[[394], []]]=42 PairPaths@BflyStart: PairPath [_paths=[[394, 396, 390], []]]=4 Start Vertex:396 PairPaths@BflyStart: PairPath [_paths=[[396, 390], []]]=4 QUEUE IS: [:W2147483647(V-1_D-1)] #### getAllProbablePaths() The next node in the queue C is -1 butterfly pct done: 1 / 3 = 33.333336% pct done. ReadsStartingAtV_START_BFLY, Node: -1 read: PairPath [_paths=[[-1, 394], []]] Exploring extension of: 1 paths that end at vertex: -1 == Current Paths Constructed Up To Vertex: -1 : PathPartialReconstruction@[-1] : [-1] Adding the reads {PairPath [_paths=[[-1, 394], []]]=1} to the path [-1] ################################################ ###### Exploring extension of v: -1 by successor: 385 ################################################ component either lacks: 385 or at sink ################################################ ###### Exploring extension of v: -1 by successor: 391 ################################################ component either lacks: 391 or at sink ################################################ ###### Exploring extension of v: -1 by successor: 394 ################################################ Count of paths ending at v: -1 = 1 path_ending_at_v: [-1] # [PathCounter(394)=0 Examining potential extension of path ending at node V: -1 by successor: 394, via path=[-1] path [-1] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 394], []]] -checking if subPath has enough read support. Exploring sub path: [394] -readsOfPathUntilV: PairPath [_paths=[[-1, 394], []]] -checking if pp: PairPath [_paths=[[-1, 394], []]] supports extension of [-1, 394] => true examining subPath: [394] for reinforcement by read: [[-1, 394], []] :true the read PairPath [_paths=[[-1, 394], []]](1) enforces the sub-path ([394]) -found: 1 reads supporting subpath. the sub-path ([394]) has PASSED Successful extension of 394 to generate path [-1, 394] updateReadsOfPath: [-1, 394] read PairPath [_paths=[[-1, 394], []]] is consistent with 394 pct_contained_propagated: 0.0% 394 was added to the queue QUEUE IS: [GAAGTTCATG...GTTTGATGAA:W21(V394_0_D0)] #### getAllProbablePaths() The next node in the queue C is 394 butterfly pct done: 2 / 3 = 66.66667% pct done. ReadsStartingAtV_START_BFLY, Node: 394 read: PairPath [_paths=[[394, 396], []]] ReadsStartingAtV_START_BFLY, Node: 394 read: PairPath [_paths=[[394], []]] ReadsStartingAtV_START_BFLY, Node: 394 read: PairPath [_paths=[[394, 396, 390], []]] Exploring extension of: 1 paths that end at vertex: 394 == Current Paths Constructed Up To Vertex: 394 : PathPartialReconstruction@[394] : [-1, 394] Adding the reads {PairPath [_paths=[[394, 396], []]]=6, PairPath [_paths=[[394], []]]=42, PairPath [_paths=[[394, 396, 390], []]]=4} to the path [-1, 394] ################################################ ###### Exploring extension of v: 394 by successor: 396 ################################################ Count of paths ending at v: 394 = 1 path_ending_at_v: [-1, 394] # [PathCounter(396)=0 Examining potential extension of path ending at node V: 394 by successor: 396, via path=[-1, 394] path [-1, 394] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1, 394] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 394], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394, 396], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394, 396, 390], []]] -checking if subPath has enough read support. Exploring sub path: [394, 396] -readsOfPathUntilV: PairPath [_paths=[[-1, 394], []]] -checking if pp: PairPath [_paths=[[-1, 394], []]] supports extension of [-1, 394, 396] => false examining subPath: [394, 396] for reinforcement by read: [[-1, 394], []] :false the read PairPath [_paths=[[-1, 394], []]](1) does not enforce the sub-path ([394, 396]) -readsOfPathUntilV: PairPath [_paths=[[394, 396], []]] -checking if pp: PairPath [_paths=[[394, 396], []]] supports extension of [-1, 394, 396] => true examining subPath: [394, 396] for reinforcement by read: [[394, 396], []] :true the read PairPath [_paths=[[394, 396], []]](6) enforces the sub-path ([394, 396]) -found: 6 reads supporting subpath. the sub-path ([394, 396]) has PASSED Successful extension of 396 to generate path [-1, 394, 396] updateReadsOfPath: [-1, 394, 396] read PairPath [_paths=[[394, 396], []]] is consistent with 396 read PairPath [_paths=[[394], []]] is consistent with 396 read PairPath [_paths=[[394, 396, 390], []]] is consistent with 396 pct_contained_propagated: 25.0% 396 was added to the queue QUEUE IS: [TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1)] #### getAllProbablePaths() The next node in the queue C is 396 butterfly pct done: 3 / 3 = 100.0% pct done. ReadsStartingAtV_START_BFLY, Node: 396 read: PairPath [_paths=[[396, 390], []]] Exploring extension of: 1 paths that end at vertex: 396 == Current Paths Constructed Up To Vertex: 396 : PathPartialReconstruction@[396] : [-1, 394, 396] Adding the reads {PairPath [_paths=[[396, 390], []]]=4} to the path [-1, 394, 396] ################################################ ###### Exploring extension of v: 396 by successor: 390 ################################################ Count of paths ending at v: 396 = 1 path_ending_at_v: [-1, 394, 396] # [PathCounter(390)=0 Examining potential extension of path ending at node V: 396 by successor: 390, via path=[-1, 394, 396] TripletMapper doesnt contain node: 396 ReadsOfPathUntilV: PATH: [-1, 394, 396] ReadsOfPathUntiV: READ: PairPath [_paths=[[396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 394], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394, 396], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394, 396, 390], []]] -checking if subPath has enough read support. Exploring sub path: [390] -readsOfPathUntilV: PairPath [_paths=[[396, 390], []]] -checking if pp: PairPath [_paths=[[396, 390], []]] supports extension of [-1, 394, 396, 390] => true examining subPath: [390] for reinforcement by read: [[396, 390], []] :true the read PairPath [_paths=[[396, 390], []]](4) enforces the sub-path ([390]) -found: 4 reads supporting subpath. the sub-path ([390]) has PASSED Successful extension of 390 to generate path [-1, 394, 396, 390] updateReadsOfPath: [-1, 394, 396, 390] read PairPath [_paths=[[396, 390], []]] is consistent with 390 read PairPath [_paths=[[394, 396, 390], []]] is consistent with 390 pct_contained_propagated: 60.000004% 390 was added to the queue QUEUE IS: [ATAAGCATAT...TATGCTTGTG:W20(V390_128_D2)] #### getAllProbablePaths() The next node in the queue C is 390 butterfly pct done: 4 / 3 = 133.33334% pct done. ReadsStartingAtV_START_BFLY, Node: 390 read: PairPath [_paths=[[390], []]] ReadsStartingAtV_START_BFLY, Node: 390 read: PairPath [_paths=[[390, -2], []]] Exploring extension of: 1 paths that end at vertex: 390 == Current Paths Constructed Up To Vertex: 390 : PathPartialReconstruction@[390] : [-1, 394, 396, 390] Adding the reads {PairPath [_paths=[[390], []]]=144, PairPath [_paths=[[390, -2], []]]=1} to the path [-1, 394, 396, 390] ################################################ ###### Exploring extension of v: 390 by successor: -2 ################################################ Count of paths ending at v: 390 = 1 path_ending_at_v: [-1, 394, 396, 390] # [PathCounter(-2)=0 Examining potential extension of path ending at node V: 390 by successor: -2, via path=[-1, 394, 396, 390] TripletMapper doesnt contain node: 390 ReadsOfPathUntilV: PATH: [-1, 394, 396, 390] ReadsOfPathUntiV: READ: PairPath [_paths=[[396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 394], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394, 396], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[394, 396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[390, -2], []]] -checking if subPath has enough read support. Exploring sub path: [390, -2] -readsOfPathUntilV: PairPath [_paths=[[396, 390], []]] -checking if pp: PairPath [_paths=[[396, 390], []]] supports extension of [-1, 394, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[396, 390], []] :false the read PairPath [_paths=[[396, 390], []]](4) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[-1, 394], []]] -checking if pp: PairPath [_paths=[[-1, 394], []]] supports extension of [-1, 394, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[-1, 394], []] :false the read PairPath [_paths=[[-1, 394], []]](1) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[394, 396], []]] -checking if pp: PairPath [_paths=[[394, 396], []]] supports extension of [-1, 394, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[394, 396], []] :false the read PairPath [_paths=[[394, 396], []]](6) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[394], []]] -checking if pp: PairPath [_paths=[[394], []]] supports extension of [-1, 394, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[394], []] :false the read PairPath [_paths=[[394], []]](42) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[394, 396, 390], []]] -checking if pp: PairPath [_paths=[[394, 396, 390], []]] supports extension of [-1, 394, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[394, 396, 390], []] :false the read PairPath [_paths=[[394, 396, 390], []]](4) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[390], []]] -checking if pp: PairPath [_paths=[[390], []]] supports extension of [-1, 394, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[390], []] :false the read PairPath [_paths=[[390], []]](144) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[390, -2], []]] -checking if pp: PairPath [_paths=[[390, -2], []]] supports extension of [-1, 394, 396, 390, -2] => true examining subPath: [390, -2] for reinforcement by read: [[390, -2], []] :true the read PairPath [_paths=[[390, -2], []]](1) enforces the sub-path ([390, -2]) -found: 1 reads supporting subpath. the sub-path ([390, -2]) has PASSED Successful extension of -2 to generate path [-1, 394, 396, 390, -2] updateReadsOfPath: [-1, 394, 396, 390, -2] read PairPath [_paths=[[390], []]] is consistent with -2 read PairPath [_paths=[[390, -2], []]] is consistent with -2 pct_contained_propagated: 71.42857% -2 was added to the queue QUEUE IS: [:W-1(V-2_D-1)] #### getAllProbablePaths() The next node in the queue C is -2 butterfly pct done: 5 / 3 = 166.66666% pct done. ReadsStartingAtV_START_BFLY-2 EMPTY Exploring extension of: 1 paths that end at vertex: -2 == Current Paths Constructed Up To Vertex: -2 : PathPartialReconstruction@[-2] : [-1, 394, 396, 390, -2] the finished path: [-1, 394, 396, 390, -2] was added to the final paths, with 202 support FinalPath@BeforeFiltering: [-1, 394, 396, 390, -2] Grouping paths into genes IsoformClustering, number of clusters = 0 Sep Gene IDs:{[-1, 394, 396, 390, -2]=1} FinalPath@AfterFiltering: [-1, 394, 396, 390, -2] Final Paths: 1 Final path reported: comp0_g3_i1 len=360 path=[394:0-126 396:127-150 390:151-359] [-1, 394, 396, 390, -2] total number of paths reported = 3 from 3 components Done make[1]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg' fakeroot debian/rules binary-arch dh binary-arch --parallel --with javahelper,autoreconf dh_testroot -a -O--parallel dh_prep -a -O--parallel debian/rules override_dh_auto_install make[1]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs; do dh_auto_install \ -O--sourcedirectory=${target}; done make -j1 install DESTDIR=/<>/trinityrnaseq-2.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm' Making install in src make[3]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fdebug-prefix-map=/<>/trinityrnaseq-2.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IRKE_run.o IRKE_run.cpp IRKE_run.cpp:9:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. Makefile:431: recipe for target 'IRKE_run.o' failed make[3]: *** [IRKE_run.o] Error 1 make[3]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm/src' Makefile:349: recipe for target 'install-recursive' failed make[2]: *** [install-recursive] Error 1 make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/Inchworm' dh_auto_install: make -j1 install DESTDIR=/<>/trinityrnaseq-2.2.0+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no returned exit code 2 make -j1 install DESTDIR=/<>/trinityrnaseq-2.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make install; done <<< src >>> make[3]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src' mv slclust ../bin/ make[3]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust' make[1]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg' debian/rules override_dh_install-arch make[1]: Entering directory '/<>/trinityrnaseq-2.2.0+dfsg' dh_install -a dh_install: Cannot find (any matches for) "Chrysalis/TranscriptomeFromVaryK" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/TranscriptomeFromVaryK dh_install: Cannot find (any matches for) "Chrysalis/RunButterfly" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/RunButterfly dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI_chang" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI_chang dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts dh_install: Cannot find (any matches for) "Chrysalis/QuantifyGraph" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/QuantifyGraph dh_install: Cannot find (any matches for) "Chrysalis/JoinTransByPairs" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/JoinTransByPairs dh_install: Cannot find (any matches for) "Chrysalis/IsoformAugment" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/IsoformAugment dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta_MPI" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta_MPI dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta dh_install: Cannot find (any matches for) "Chrysalis/CreateIwormFastaBundle" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/CreateIwormFastaBundle dh_install: Cannot find (any matches for) "Chrysalis/Chrysalis" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/Chrysalis dh_install: Cannot find (any matches for) "Chrysalis/BreakTransByPairs" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: Chrysalis/BreakTransByPairs dh_install: Cannot find (any matches for) "debian/tmp/usr/lib/trinityrnaseq/Inchworm" (tried in "." and "debian/tmp") dh_install: trinityrnaseq missing files: debian/tmp/usr/lib/trinityrnaseq/Inchworm dh_install: missing files, aborting debian/rules:47: recipe for target 'override_dh_install-arch' failed make[1]: *** [override_dh_install-arch] Error 255 make[1]: Leaving directory '/<>/trinityrnaseq-2.2.0+dfsg' debian/rules:20: recipe for target 'binary-arch' failed make: *** [binary-arch] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2016-08-29T15:52:08Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 0 Build-Time: 22 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 43 Job: trinityrnaseq_2.2.0+dfsg-2 Machine Architecture: amd64 Package: trinityrnaseq Package-Time: 99 Source-Version: 2.2.0+dfsg-2 Space: 0 Status: failed Version: 2.2.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2016-08-29T15:52:08Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 99.929908636s DC-Time-Estimation: 99.929908636 versus expected 986 (r/m: 8.86691585590814 ; m: 99.929908636)